GROMACS教程：漏斗网蜘蛛毒素肽的溶剂化研究：Amber99SB-ILDN力场

Using the Amber99sb-ildn force field in directory C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff

Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\aminoacids.r2b
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\dna.r2b
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\rna.r2b
Reading fws.pdb...
Read 'OMEGA-AGA-IVB', 257 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 38 residues with 257 atoms

  chain  #res #atoms
  1 'A'    35    257

All occupancies are one
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\atomtypes.atp
Atomtype 1
Reading residue database... (amber99sb-ildn)
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\dna.rtp
Residue 109
Sorting it all out...
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\rna.rtp
Residue 125
Sorting it all out...
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\aminoacids.hdb
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\dna.hdb
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\rna.hdb
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\aminoacids.n.tdb
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\aminoacids.c.tdb
Processing chain 1 'A' (257 atoms, 35 residues)
Identified residue CYS4 as a starting terminus.
Identified residue PRO38 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
					CYS4   CYS12   CYS19   CYS20   CYS25   CYS27   MET29
					 SG6    SG67   SG118   SG124   SG163   SG180   SD193
   CYS12    SG67   1.202
   CYS19   SG118   0.727   0.705
   CYS20   SG124   0.202   1.267   0.730
   CYS25   SG163   1.159   0.202   0.570   1.197
   CYS27   SG180   1.813   0.627   1.223   1.854   0.666
   MET29   SD193   2.596   1.490   1.906   2.622   1.466   0.949
   CYS34   SG227   1.742   0.540   1.200   1.804   0.636   0.202   1.079
   CYS36   SG242   0.928   0.645   0.202   0.930   0.478   1.089   1.718
				   CYS34
				   SG227
   CYS36   SG242   1.085
Linking CYS-4 SG-6 and CYS-20 SG-124...
Linking CYS-12 SG-67 and CYS-25 SG-163...
Linking CYS-19 SG-118 and CYS-36 SG-242...
Linking CYS-27 SG-180 and CYS-34 SG-227...
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\aminoacids.arn
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\dna.arn
Opening force field file C:/Users/Jicun/E_Prf/Gromacs-4.6/share/top/amber99sb-ildn.ff\rna.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 35 residues with 495 atoms
Making bonds...
Number of bonds was 504, now 503
Generating angles, dihedrals and pairs...
Before cleaning: 1314 pairs
Before cleaning: 1356 dihedrals
Keeping all generated dihedrals
Making cmap torsions...There are 1356 dihedrals,   99 impropers,  906 angles
		  1308 pairs,      503 bonds and     0 virtual sites
Total mass 3798.434 a.m.u.
Total charge 2.000 e
Writing topology

Writing coordinate file...
				--------- PLEASE NOTE ------------
You have successfully generated a topology from: fws.pdb.
The Amber99sb-ildn force field and the tip3p water model are used.
				--------- ETON ESAELP ------------

gcq#37: "Never Get a Chance to Kick Ass" (The Amps)

Read 495 atoms
Volume: 0.001 nm^3, corresponds to roughly 0 electrons
No velocities found
	system size :  2.793  1.951  2.502 (nm)
	diameter    :  3.319               (nm)
	center      : -0.156 -2.386 -0.412 (nm)
	box vectors :  0.100  0.100  0.100 (nm)
	box angles  :  90.00  90.00  90.00 (degrees)
	box volume  :   0.00               (nm^3)
	shift       :  4.445  6.675  2.434 (nm)
new center      :  4.289  4.289  2.022 (nm)
new box vectors :  5.719  5.719  5.719 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  : 132.24               (nm^3)

gcq#178: "Whatever Happened to Pong ?" (F. Black)

Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

NOTE 1 [file fws.top, line 4775]:
  System has non-zero total charge: 2.000000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.

Analysing residue names:
There are:    35    Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 1482.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 48x48x48, spacing 0.119 0.119 0.119
Estimate for the relative computational load of the PME mesh part: 0.83

NOTE 2 [file em-vac-pme.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing.

This run will generate roughly 1 Mb of data

There were 2 notes

gcq#75: "Hold On Like Cliffhanger" (Urban Dance Squad)

NOTE 1 [file em-vac-pme.mdp, line 22]:
  em-vac-pme.mdp did not specify a value for the .mdp option
  "cutoff-scheme". Probably it was first intended for use with GROMACS
  before 4.6. In 4.6, the Verlet scheme was introduced, but the group
  scheme was still the default. The default is now the Verlet scheme, so
  you will observe different behaviour.
NOTE 2 [file em-vac-pme.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 108284530
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
NOTE 3 [file fws.top, line 4771]:
  System has non-zero total charge: 2.000000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.
  Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:    35    Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 1482.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 48x48x48, spacing 0.119 0.119 0.119
Estimate for the relative computational load of the PME mesh part: 0.85
NOTE 4 [file em-vac-pme.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing.
This run will generate roughly 1 Mb of data
There were 4 notes
gcq#553: "Should we force science down the throats of those that have no taste for it? Is it our duty to drag them kicking and screaming into the twenty-first century? I am afraid that it is." (George Porter)

Reading file em-vac.tpr, VERSION 4.6.2-dev (single precision)
Using 4 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine, which is better)

Steepest Descents:
   Tolerance (Fmax)   = 5.00000e+002
   Number of steps    =         1000
Step=    0, Dmax= 1.0e-002 nm, Epot= 1.41200e+003 Fmax= 5.70923e+003, atom= 150
Step=    1, Dmax= 1.0e-002 nm, Epot= -2.24422e+002 Fmax= 4.54461e+003, atom= 164
Step=    3, Dmax= 6.0e-003 nm, Epot= -7.68675e+002 Fmax= 3.09902e+003, atom= 150
Step=    4, Dmax= 7.2e-003 nm, Epot= -7.84120e+002 Fmax= 5.49768e+003, atom= 164
Step=    5, Dmax= 8.6e-003 nm, Epot= -8.30759e+002 Fmax= 5.95529e+003, atom= 164
......
Step=   98, Dmax= 2.1e-003 nm, Epot= -1.77253e+003 Fmax= 3.70245e+002, atom= 494

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 500 in 99 steps
Potential Energy  = -1.7725271e+003
Maximum force     = 3.7024463e+002 on atom 494
Norm of force     = 7.0873062e+001

gcq#313: "My Brothers are Protons (Protons!), My Sisters are Neurons (Neurons)" (Gogol Bordello)

Running on 1 node with total 2 cores, 4 logical cores
Hardware detected:
  CPU info:
    Vendor: GenuineIntel
    Brand:  Intel(R) Core(TM) i5-4210U CPU @ 1.70GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: SSE2
Compiled SIMD instructions: SSE2, GROMACS could use AVX2_256 on this machine, which is better
Reading file em-vac.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads
Steepest Descents:
   Tolerance (Fmax)   =  5.00000e+02
   Number of steps    =         1000
Step=    0, Dmax= 1.0e-02 nm, Epot=  1.45219e+03 Fmax= 5.70926e+03, atom= 150
Step=    1, Dmax= 1.0e-02 nm, Epot= -1.83565e+02 Fmax= 4.54459e+03, atom= 164
Step=    3, Dmax= 6.0e-03 nm, Epot= -7.28101e+02 Fmax= 3.09905e+03, atom= 150
Step=    4, Dmax= 7.2e-03 nm, Epot= -7.40962e+02 Fmax= 5.49785e+03, atom= 164
Step=    5, Dmax= 8.6e-03 nm, Epot= -7.86727e+02 Fmax= 5.95532e+03, atom= 164
......
Step=   98, Dmax= 2.1e-03 nm, Epot= -1.73279e+03 Fmax= 3.70232e+02, atom= 494
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 500 in 99 steps
Potential Energy  = -1.7327905e+03
Maximum force     =  3.7023245e+02 on atom 494
Norm of force     =  7.0877754e+01
gcq#189: "It's So Fast It's Slow" (F. Black)

Reading solute configuration
OMEGA-AGA-IVB
Containing 495 atoms in 35 residues
Initialising van der waals distances...

WARNING: Masses and atomic (Van der Waals) radii will be guessed
		 based on residue and atom names, since they could not be
		 definitively assigned from the information in your input
		 files. These guessed numbers might deviate from the mass
		 and radius of the atom type. Please check the output
		 files if necessary.

Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 4x4x3 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
	SOL (   3 atoms): 10368 residues
Calculating Overlap...
box_margin = 0.315
Removed 15591 atoms that were outside the box
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
System total charge: 0.000
Potential shift: LJ r^-12: 0.000 r^-6 0.000, Coulomb 0.000

Grid: 16 x 16 x 12 cells
Successfully made neighbourlist
nri = 48244, nrj = 2096044
Checking Protein-Solvent overlap: tested 10693 pairs, removed 522 atoms.
Checking Solvent-Solvent overlap: tested 189380 pairs, removed 2823 atoms.
Added 4056 molecules
Generated solvent containing 12168 atoms in 4056 residues
Writing generated configuration to fws-b4ion.gro
OMEGA-AGA-IVB

Output configuration contains 12663 atoms in 4091 residues
Volume                 :      132.24 (nm^3)
Density                :     968.242 (g/l)
Number of SOL molecules:   4056

Processing topology
Adding line for 4056 solvent molecules to topology file (fws.top)

Back Off! I just backed up fws.top to ./#fws.top.1#

gcq#255: "In the End Science Comes Down to Praying" (P. v.d. Berg)

Reading solute configuration
OMEGA-AGA-IVB
Containing 495 atoms in 35 residues
Reading solvent configuration and velocities
216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
Containing 648 atoms in 216 residues
Initialising inter-atomic distances...
WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.
NOTE: From version 5.0 gmx uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
-------- -------- --- Thank You --- -------- --------
Generating solvent configuration
Will generate new solvent configuration of 4x4x3 boxes
Solvent box contains 15741 atoms in 5247 residues
Removed 3276 solvent atoms due to solvent-solvent overlap
Removed 480 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms):  3995 residues
Generated solvent containing 11985 atoms in 3995 residues
Writing generated configuration to fws-b4ion.gro
Output configuration contains 12480 atoms in 4030 residues
Volume                 :      132.24 (nm^3)
Density                :     954.442 (g/l)
Number of SOL molecules:   3995
Processing topology
Back Off! I just backed up temp.topleIpfl to ./#temp.topleIpfl.1#
Adding line for 3995 solvent molecules to topology file (fws.top)
Back Off! I just backed up fws.top to ./#fws.top.1#
gcq#195: "Just Give Me a Blip" (F. Black)

NOTE 1 [file em-sol-pme.mdp, line 20]:
  em-sol-pme.mdp did not specify a value for the .mdp option
  "cutoff-scheme". Probably it was first intended for use with GROMACS
  before 4.6. In 4.6, the Verlet scheme was introduced, but the group
  scheme was still the default. The default is now the Verlet scheme, so
  you will observe different behaviour.
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
NOTE 2 [file em-sol-pme.mdp]:  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note  that with the Verlet scheme, nstlist has no effect on the accuracy of  your simulation.
Setting the LD random seed to 3225797633
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 3 [file fws.top, line 4772]:
  System has non-zero total charge: 2.000000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:    35    Protein residues
There are:  3995      Water residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 37437.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 48x48x48, spacing 0.119 0.119 0.119
Estimate for the relative computational load of the PME mesh part: 0.20
This run will generate roughly 6 Mb of data
There were 3 notes
gcq#250: "Wicky-wicky Wa-wild West" (Will Smith)

Reading file ion.tpr, VERSION 5.1.2 (single precision)
Reading file ion.tpr, VERSION 5.1.2 (single precision)
Will try to add 12 NA ions and 14 CL ions.
Select a continuous group of solvent molecules
Group     0 (         System) has 12480 elements
Group     1 (        Protein) has   495 elements
Group     2 (      Protein-H) has   257 elements
Group     3 (        C-alpha) has    35 elements
Group     4 (       Backbone) has   105 elements
Group     5 (      MainChain) has   141 elements
Group     6 (   MainChain+Cb) has   171 elements
Group     7 (    MainChain+H) has   176 elements
Group     8 (      SideChain) has   319 elements
Group     9 (    SideChain-H) has   116 elements
Group    10 (    Prot-Masses) has   495 elements
Group    11 (    non-Protein) has 11985 elements
Group    12 (          Water) has 11985 elements
Group    13 (            SOL) has 11985 elements
Group    14 (      non-Water) has   495 elements
Select a group:
> 13
Selected 13: 'SOL'
Number of (3-atomic) solvent molecules: 3995
Processing topology
Back Off! I just backed up temp.topoGPO9o to ./#temp.topoGPO9o.1#
Replacing 26 solute molecules in topology file (fws.top)  by 12 NA and 14 CL ions.
Back Off! I just backed up fws.top to ./#fws.top.2#
Replacing solvent molecule 401 (atom 1698) with NA
Replacing solvent molecule 1112 (atom 3831) with NA
Replacing solvent molecule 876 (atom 3123) with NA
Replacing solvent molecule 3640 (atom 11415) with NA
Replacing solvent molecule 3719 (atom 11652) with NA
Replacing solvent molecule 634 (atom 2397) with NA
Replacing solvent molecule 1323 (atom 4464) with NA
Replacing solvent molecule 175 (atom 1020) with NA
Replacing solvent molecule 817 (atom 2946) with NA
Replacing solvent molecule 3477 (atom 10926) with NA
Replacing solvent molecule 672 (atom 2511) with NA
Replacing solvent molecule 3897 (atom 12186) with NA
Replacing solvent molecule 2026 (atom 6573) with CL
Replacing solvent molecule 2185 (atom 7050) with CL
Replacing solvent molecule 2899 (atom 9192) with CL
Replacing solvent molecule 1936 (atom 6303) with CL
Replacing solvent molecule 2280 (atom 7335) with CL
Replacing solvent molecule 737 (atom 2706) with CL
Replacing solvent molecule 1901 (atom 6198) with CL
Replacing solvent molecule 3831 (atom 11988) with CL
Replacing solvent molecule 2233 (atom 7194) with CL
Replacing solvent molecule 2808 (atom 8919) with CL
Replacing solvent molecule 3350 (atom 10545) with CL
Replacing solvent molecule 2666 (atom 8493) with CL
Replacing solvent molecule 2299 (atom 7392) with CL
Replacing solvent molecule 2742 (atom 8721) with CL
gcq#171: "That Was Pretty Cool" (Beavis)

NOTE 1 [file em-sol-pme.mdp, line 20]:
  em-sol-pme.mdp did not specify a value for the .mdp option
  "cutoff-scheme". Probably it was first intended for use with GROMACS
  before 4.6. In 4.6, the Verlet scheme was introduced, but the group
  scheme was still the default. The default is now the Verlet scheme, so
  you will observe different behaviour.
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
NOTE 2 [file em-sol-pme.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.
Setting the LD random seed to 808809886
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
Excluding 1 bonded neighbours molecule type 'CL'
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:    35    Protein residues
There are:  3969      Water residues
There are:    26        Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 37281.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 48x48x48, spacing 0.119 0.119 0.119
Estimate for the relative computational load of the PME mesh part: 0.20
This run will generate roughly 6 Mb of data
There were 2 notes
gcq#323: "I managed to get two hours of work done before work" (E. Lindahl)

Steepest Descents converged to Fmax < 1000 in 207 steps
Potential Energy  = -1.8840495e+05
Maximum force     =  9.8538837e+02 on atom 109
Norm of force     =  5.3166636e+03

Steepest Descents:
   Tolerance (Fmax)   =  2.50000e+02
   Number of steps    =         5000
Step=    0, Dmax= 1.0e-02 nm, Epot= -6.33612e+04 Fmax= 3.90439e+05, atom= 3703
Step=    1, Dmax= 1.0e-02 nm, Epot= -7.90314e+04 Fmax= 1.08842e+05, atom= 3703
......
Step= 3353, Dmax= 1.9e-03 nm, Epot= -2.13599e+05 Fmax= 2.44805e+02, atom= 64
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 250 in 3354 steps
Potential Energy  = -2.1359919e+05
Maximum force     =  2.4480508e+02 on atom 64
Norm of force     =  8.9025946e+00
NOTE: 18 % of the run time was spent in pair search,
      you might want to increase nstlist (this has no effect on accuracy)
gcq#101: "The World is a Friendly Place" (Magnapop)

			   Core t (s)   Wall t (s)        (%)
	   Time:     2858.203     2858.000      100.0
						 47:38
				 (ns/day)    (hour/ns)
Performance:       30.231        0.794

Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
  1  Angle            2  Proper-Dih.      3  Improper-Dih.    4  LJ-14
  5  Coulomb-14       6  LJ-(SR)          7  Disper.-corr.    8  Coulomb-(SR)
  9  Coul.-recip.    10  Potential       11  Kinetic-En.     12  Total-Energy
 13  Temperature     14  Pres.-DC        15  Pressure        16  Constr.-rmsd
 17  Box-X           18  Box-Y           19  Box-Z           20  Volume
 21  Density         22  pV              23  Enthalpy        24  Vir-XX
 25  Vir-XY          26  Vir-XZ          27  Vir-YX          28  Vir-YY
 29  Vir-YZ          30  Vir-ZX          31  Vir-ZY          32  Vir-ZZ
 33  Pres-XX         34  Pres-XY         35  Pres-XZ         36  Pres-YX
 37  Pres-YY         38  Pres-YZ         39  Pres-ZX         40  Pres-ZY
 41  Pres-ZZ         42  #Surf*SurfTen   43  Box-Vel-XX      44  Box-Vel-YY
 45  Box-Vel-ZZ                          46  Coul-SR:Protein-Protein
 47  LJ-SR:Protein-Protein               48  Coul-14:Protein-Protein
 49  LJ-14:Protein-Protein               50  Coul-SR:Protein-non-Protein
 51  LJ-SR:Protein-non-Protein           52  Coul-14:Protein-non-Protein
 53  LJ-14:Protein-non-Protein           54  Coul-SR:non-Protein-non-Protein
 55  LJ-SR:non-Protein-non-Protein       56  Coul-14:non-Protein-non-Protein
 57  LJ-14:non-Protein-non-Protein       58  T-Protein
 59  T-non-Protein                       60  Lamb-Protein
 61  Lamb-non-Protein

Statistics over 500001 steps [ 0.0000 through 1000.0000 ps ], 4 data sets
All statistics are over 5001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Potential                   -176225         13     417.02    80.6394  (kJ/mol)
Kinetic En.                 31467.9        5.6    275.731   0.780693  (kJ/mol)
Total Energy                -144758         13    492.513    81.4195  (kJ/mol)
Temperature                 299.932      0.053    2.62809 0.00744002  (K)

Statistics over 500001 steps [ 0.0000 through 1000.0000 ps ], 4 data sets
All statistics are over 5001 points
Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Potential                   -173825         20    432.623   -85.8249  (kJ/mol)
Kinetic En.                 31031.6        6.5    299.416    -33.179  (kJ/mol)
Total Energy                -142793         26    556.977   -119.003  (kJ/mol)
Temperature                 300.129      0.063    2.89586  -0.320896  (K)
gcq#155: "I Am a Wonderful Thing" (Kid Creole)

pymol bfactors.pdb
hide everything
show cartoon
spectrum b

Q = XXX
cmd.alter("all", "q = b > Q and Q or b")
spectrum q

ray 1200,1200
png bfac.png, dpi=300

pymol clusters.pdb
split_states clusters
delete clusters
dss
show cartoon