Re: Trajectory analysis

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Oct 18 2006 - 12:06:57 CDT

Hi Philip,
the previous case was solved by using the version of NAMDEnergy in
VMD1.8.5 together with NAMD2.6; the earlier versions didn't work
properly with periodic cells.
Since you're doing postprocessing, a number of the parameters in your
config file are unnecessary, and may be causing problems. Remember that
during this sort of postprocessing there won't be any coordinate
movement, so at the very least, the rigidbonds, and your temperature and
pressure controls, should not be there. You might want to look at the
input files written by the NAMDEnergy plugin (from VMD1.8.5, and using
periodic conditions) with the debug option turned on -- you should only
add options in addition to the ones written in that file if you have a
*really* good reason. You can also see the last example at
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node42.html for a similar
case. Let me know if you still have problems after these changes.
Best,
Peter

Philip Blood wrote:
> Hi,
>
> Was there a resolution to this problem? I have run across a similar
> problem doing trajectory analysis in NAMD2.6b1 (currently running on
> NCSA IA-64). I found that when analyzing an NPT trajectory using the
> Tcl functions and reading in a dcd file, it appears that NAMD does not
> update the cell dimensions when it calculates the forces. This is
> manifested in a number of ways: first, I expected that when analyzing
> the dcd I would not need to worry about entering the precise cell
> dimensions into the NAMD configuration file since it would read them
> from the dcd. This, however, resulted in immediate constraint
> failures. So I entered the exact cell dimensions in the configuration
> file (obtained from the .xst file from the simulation that generated
> the dcd), and the simulation ran for a few steps and then failed with
> constraint failures. In the initial step the energy looks perfect.
> If I turn off rigidBonds, I see the same problem mentioned below: the
> analysis runs, but eventually the energies become huge.
>
> I used the getcell command in a tclBC script to check the cell
> dimensions, and NAMD is reading them correctly, but for some reason is
> not using them when it calculates the force--I believe it just uses
> the original ones that I input directly into the configuration file
> for the purpose of calculating the forces and energy. In addition, my
> colleague has done something similar and obtained the same result,
> however, if she then ran the same analysis on an NVT simulation
> trajectory everything was perfect.
>
> Here is that script and the output that shows it reading the right
> cell dimensions but then terminating with constraint failures. Again,
> if I remove the rigidBonds it continues to run, but the energies blow up.
> Thanks,
> Phil Blood
>
> source source.file
>
> #firsttimestep $first
> #numsteps $numsteps
>
> temperature 310K
> seed 40277
>
> coordinates $dir0/$name.pdb
> #bincoordinates $dir0/$name.$id0.restart.coor
> #binvelocities $dir0/$name.$id0.restart.vel
>
> structure $dir0/$name.xplor.psf
>
> parameters $dir0/par_dops.inp
> paraTypeCharmm on
>
> cellBasisVector1 459.122 0.0 0.0
> cellBasisVector2 0.0 93.9624 0.0
> cellBasisVector3 0.0 0.0 167.397
> #extendedSystem $dir0/$name.$id0.restart.xsc
> XSTfile $scrdir/$name.$id.xst
> XSTfreq 500
> wrapAll on
>
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 10.0
> cutoff 12.0
> pairlistdist 13.5
> stepspercycle 20
> #stepspercycle 1
> rigidBonds all
> rigidTolerance 1.0e-8
>
> #PME options
> PME yes
> PMETolerance 1.0e-6
> PMEInterpOrder 6
> PMEGridSizeX 486
> PMEGridSizeY 100
> PMEGridSizeZ 150
>
> # pressure control
> useGroupPressure yes
> useFlexibleCell yes
> useConstantRatio no
> useConstantArea no
> LangevinPiston on
> LangevinPistonTarget 1.01325
> LangevinPistonPeriod 2000
> LangevinPistonDecay 2000
> LangevinPistonTemp 310
>
> # temperature control
> langevin on
> langevinTemp 310
> langevinDamping 0.5
>
>
>
> fullElectFrequency 1
> timestep 2.0
>
> # output params
> outputname $scrdir/$name.$id
> #outputEnergies 500
> #outputMomenta 500
> #outputPressure 500
>
> # outputTiming
> #binaryoutput no
> #DCDfile $dcddir/$name.$id.dcd
> #DCDfreq 500
> DCDUnitCell yes
> #velDCDfile $dcddir/$name.$id.veldcd
> #velDCDfreq 500
> #restartname $scrdir/$name.$id.restart
> #restartfreq 500
>
> tclBC on
>
> #files for input and output
> set inputdcd $dir0/$name.$id.dcd
> set ftmp $scrdir/$name.fout.$id.dat
> set f_outfile [open $ftmp w]
>
> tclBCScript {
> proc calcforces {step unique} {
>
> set mycell [getcell]
> print $mycell
>
> while {[nextatom]} {
>
> } }
> }
>
> set ts 500
> firstTimestep $ts
> set maxstep 50000
> coorfile open dcd $inputdcd
>
> while { ![coorfile read] && $ts < $maxstep } {
> # Compute energies and forces, but don't try to move the atoms.
> run 0
> puts "reading timestep $ts"
> incr ts 500
> firstTimestep $ts }
>
> run 0
>
> close $f_outfile
>
>
> Info: NAMD 2.6b1 for Linux-ia64-MPI-GM
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
> Info:
> Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 50900 for mpi-linux-ia64
> Info: Built Fri Jul 29 11:37:35 CDT 2005 by jphillip on tg-login2
> Info: Sending usage information to NAMD developers via UDP. Sent data
> is:
> Info: 1 NAMD 2.6b1 Linux-ia64-MPI-GM 4 tg-c062 philipblood
> Info: Running on 4 processors.
> Info: 20819 kB of memory in use.
> Info: Changed directory to
> /home/philipblood/work/bar/force-match/nbar_dops.10x2.fm
> Info: Configuration file is d.namd
> TCL: Suspending until startup complete.
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 2
> Info: NUMBER OF STEPS 500
> Info: STEPS PER CYCLE 20
> Info: PERIODIC CELL BASIS 1 459.122 0 0
> Info: PERIODIC CELL BASIS 2 0 93.9624 0
> Info: PERIODIC CELL BASIS 3 0 0 167.397
> Info: PERIODIC CELL CENTER 0 0 0
> Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
> Info: LOAD BALANCE STRATEGY Other
> Info: LDB PERIOD 4000 steps
> Info: FIRST LDB TIMESTEP 100
> Info: LDB BACKGROUND SCALING 1
> Info: HOM BACKGROUND SCALING 1
> Info: PME BACKGROUND SCALING 1
> Info: MAX SELF PARTITIONS 50
> Info: MAX PAIR PARTITIONS 20
> Info: SELF PARTITION ATOMS 125
> Info: PAIR PARTITION ATOMS 200
> Info: PAIR2 PARTITION ATOMS 400
> Info: MIN ATOMS PER PATCH 100
> Info: INITIAL TEMPERATURE 310
> Info: CENTER OF MASS MOVING? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: 1-4 SCALE FACTOR 1
> Info: NO DCD TRAJECTORY OUTPUT
> Info: XST FILENAME
> /disks/scratchgpfs1/philipblood/nbar_dops.10x2.fm/339492.d179/nbar_dops.10x2.fm.d179.xst
>
> Info: XST FREQUENCY 500
> Info: NO VELOCITY DCD OUTPUT
> Info: OUTPUT FILENAME
> /disks/scratchgpfs1/philipblood/nbar_dops.10x2.fm/339492.d179/nbar_dops.10x2.fm.d179
>
> Info: BINARY OUTPUT FILES WILL BE USED
> Info: NO RESTART FILE
> Info: SWITCHING ACTIVE
> Info: SWITCHING ON 10
> Info: SWITCHING OFF 12
> Info: PAIRLIST DISTANCE 13.5
> Info: PAIRLIST SHRINK RATE 0.01
> Info: PAIRLIST GROW RATE 0.01
> Info: PAIRLIST TRIGGER 0.3
> Info: PAIRLISTS PER CYCLE 2
> Info: PAIRLISTS ENABLED
> Info: MARGIN 0.96
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 16.96
> Info: TCL BOUNDARY FORCES ACTIVE
> Info: TCL BOUNDARY FORCES SCRIPT proc calcforces {step unique} {
>
> set mycell [getcell]
> print $mycell
>
> while {[nextatom]} {
>
> }
> }
>
>
> Info: TCL BOUNDARY FORCES ARGS Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE 310
> Info: LANGEVIN DAMPING COEFFICIENT IS 0.5 INVERSE PS
> Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
> Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
> Info: TARGET PRESSURE IS 1.01325 BAR
> Info: OSCILLATION PERIOD IS 2000 FS
> Info: DECAY TIME IS 2000 FS
> Info: PISTON TEMPERATURE IS 310 K
> Info: PRESSURE CONTROL IS GROUP-BASED
> Info: INITIAL STRAIN RATE IS 0 0 0
> Info: CELL FLUCTUATION IS ANISOTROPIC
> Info: PARTICLE MESH EWALD (PME) ACTIVE
> Info: PME TOLERANCE 1e-06
> Info: PME EWALD COEFFICIENT 0.257952
> Info: PME INTERPOLATION ORDER 6
> Info: PME GRID DIMENSIONS 486 100 150
> Info: Attempting to read FFTW data from
> FFTW_NAMD_2.6b1_Linux-ia64-MPI-GM.txt
> Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
> Info: Writing FFTW data to FFTW_NAMD_2.6b1_Linux-ia64-MPI-GM.txt
> Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1
> Info: USING VERLET I (r-RESPA) MTS SCHEME.
> Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
> Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
> Info: RIGID BONDS TO HYDROGEN : ALL
> Info: ERROR TOLERANCE : 1e-08
> Info: MAX ITERATIONS : 100
> Info: RIGID WATER USING SETTLE ALGORITHM
> Info: RANDOM NUMBER SEED 40277
> Info: USE HYDROGEN BONDS? NO
> Info: COORDINATE PDB
> /home/philipblood/work/bar/force-match/nbar_dops.10x2.fm/nbar_dops.10x2.fm.pdb
>
> Info: STRUCTURE FILE
> /home/philipblood/work/bar/force-match/nbar_dops.10x2.fm/nbar_dops.10x2.fm.xplor.psf
>
> Info: PARAMETER file: CHARMM format!
> Info: PARAMETERS
> /home/philipblood/work/bar/force-match/nbar_dops.10x2.fm/par_dops.inp
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> Info: FIRST TIMESTEP 500
> Info: SUMMARY OF PARAMETERS:
> Info: 181 BONDS
> Info: 454 ANGLES
> Info: 570 DIHEDRAL
> Info: 46 IMPROPER
> Info: 114 VDW
> Info: 0 VDW_PAIRS
> Warning: Ignored 177536 bonds with zero force constants.
> Warning: Will get H-H distance in rigid H2O from H-O-H angle.
> Info: ****************************
> Info: STRUCTURE SUMMARY:
> Info: 737674 ATOMS
> Info: 557330 BONDS
> Info: 562792 ANGLES
> Info: 534758 DIHEDRALS
> Info: 4718 IMPROPERS
> Info: 0 EXCLUSIONS
> Info: 654538 RIGID BONDS
> Info: 1558484 DEGREES OF FREEDOM
> Info: 260672 HYDROGEN GROUPS
> Info: TOTAL MASS = 4.42599e+06 amu
> Info: TOTAL CHARGE = 0.000193976 e
> Info: *****************************
> Info: Entering startup phase 0 with 208622 kB of memory in use.
> Info: Entering startup phase 1 with 208622 kB of memory in use.
> Info: Entering startup phase 2 with 327085 kB of memory in use.
> Info: Entering startup phase 3 with 332861 kB of memory in use.
> Info: PATCH GRID IS 27 (PERIODIC) BY 5 (PERIODIC) BY 9 (PERIODIC)
> Info: REMOVING COM VELOCITY -0.00906089 0.00136749 -0.00782743
> Info: LARGEST PATCH (674) HAS 1093 ATOMS
> Info: Entering startup phase 4 with 428219 kB of memory in use.
> Info: PME using 4 and 4 processors for FFT and reciprocal sum.
> Info: PME GRID LOCATIONS: 0 1 2 3
> Info: PME TRANS LOCATIONS: 0 1 2 3
> Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
> Info: Entering startup phase 5 with 442739 kB of memory in use.
> Info: Entering startup phase 6 with 376170 kB of memory in use.
> Measuring processor speeds... Done.
> Info: Entering startup phase 7 with 376263 kB of memory in use.
> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> Info: NONBONDED TABLE SIZE: 769 POINTS
> Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 2.64698e-23 AT 11.9138
> Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.40436e-16 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 4.10282e-22 AT 11.9138
> Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 3.56912e-15 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.75 AT 0.0441942
> Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-14 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 19968 AT 0.0441942
> Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 6.16499e-15 AT 0.0441942
> Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-25 AT 11.8295
> Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-26 AT 11.9138
> Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-16 AT 11.9138
> Info: Entering startup phase 8 with 409365 kB of memory in use.
> Info: Finished startup with 450695 kB of memory in use.
> Info: Coordinate file
> /home/philipblood/work/bar/force-match/nbar_dops.10x2.fm/nbar_dops.10x2.fm.d179.dcd
> opened for reading.
> Info: Reading timestep from file.
> Info: Updating unit cell from timestep.
> Info: REMOVING COM VELOCITY -0.00906089 0.00136749 -0.00782743
> TCL: Running for 0 steps
> TCL: {0.0 0.0 0.0} {459.122253418 0.0 0.0} {-0.0 93.9624481201 0.0}
> {-0.0 -0.0 167.396759033}
> TCL: {0.0 0.0 0.0} {459.122253418 0.0 0.0} {-0.0 93.9624481201 0.0}
> {-0.0 -0.0 167.396759033}
> TCL: {0.0 0.0 0.0} {459.122253418 0.0 0.0} {-0.0 93.9624481201 0.0}
> {-0.0 -0.0 167.396759033}
> TCL: {0.0 0.0 0.0} {459.122253418 0.0 0.0} {-0.0 93.9624481201 0.0}
> {-0.0 -0.0 167.396759033}
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 500 24056.0398 122674.8128 54536.6888
> 1200.1142 -2235410.8602 113094.2910 0.0000
> 0.0000 480348.6491 -1439500.2646 310.2020
> -1436969.0327 -1436969.0327 310.2020 -26.5192
> -25.0174 7221538.1875 -26.5192 -25.0174
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> reading timestep 500
> TCL: Setting parameter firstTimestep to 1000
> Info: Reading timestep from file.
> Info: Updating unit cell from timestep.
> Info: REMOVING COM VELOCITY -0.00906089 0.00136749 -0.00782743
> TCL: Running for 0 steps
> TCL: {0.0 0.0 0.0} {458.889312744 0.0 0.0} {-0.0 94.0012283325 0.0}
> {-0.0 -0.0 167.454818726}
> TCL: {0.0 0.0 0.0} {458.889312744 0.0 0.0} {-0.0 94.0012283325 0.0}
> {-0.0 -0.0 167.454818726}
> TCL: {0.0 0.0 0.0} {458.889312744 0.0 0.0} {-0.0 94.0012283325 0.0}
> {-0.0 -0.0 167.454818726}
> TCL: {0.0 0.0 0.0} {458.889312744 0.0 0.0} {-0.0 94.0012283325 0.0}
> {-0.0 -0.0 167.454818726}
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 1000 24673.4115 123142.5547 54331.6447
> 1211.3140 -2237759.5570 115041.8421 0.0000
> 0.0000 480753.6046 -1438605.1854 310.4635
> -1436057.1778 -1436120.0866 310.4635 16.4442
> 17.2117 7223357.6970 16.4442 17.2117
>
> reading timestep 1000
> TCL: Setting parameter firstTimestep to 1500
> Info: Reading timestep from file.
> Info: Updating unit cell from timestep.
> Info: REMOVING COM VELOCITY -0.00906089 0.00136749 -0.00782743
> TCL: Running for 0 steps
> TCL: {0.0 0.0 0.0} {458.79006958 0.0 0.0} {-0.0 93.9584503174 0.0}
> {-0.0 -0.0 167.486663818}
> TCL: {0.0 0.0 0.0} {458.79006958 0.0 0.0} {-0.0 93.9584503174 0.0}
> {-0.0 -0.0 167.486663818}
> TCL: {0.0 0.0 0.0} {458.79006958 0.0 0.0} {-0.0 93.9584503174 0.0}
> {-0.0 -0.0 167.486663818}
> TCL: {0.0 0.0 0.0} {458.79006958 0.0 0.0} {-0.0 93.9584503174 0.0}
> {-0.0 -0.0 167.486663818}
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 1500 25155.0185 123729.6189 54457.3885
> 1228.1731 -2237642.8195 114782.3239 0.0000
> 0.0000 480551.7452 -1437738.5514 310.3332
> -1435167.5579 -1435312.7320 310.3332 159.5641
> 159.0790 7219881.7776 159.5641 159.0790
>
> reading timestep 1500
> TCL: Setting parameter firstTimestep to 2000
> Info: Reading timestep from file.
> Info: Updating unit cell from timestep.
> Info: REMOVING COM VELOCITY -0.00906089 0.00136749 -0.00782743
> TCL: Running for 0 steps
> TCL: {0.0 0.0 0.0} {459.304840088 0.0 0.0} {-0.0 93.8790893555 0.0}
> {-0.0 -0.0 167.392944336}
> TCL: {0.0 0.0 0.0} {459.304840088 0.0 0.0} {-0.0 93.8790893555 0.0}
> {-0.0 -0.0 167.392944336}
> TCL: {0.0 0.0 0.0} {459.304840088 0.0 0.0} {-0.0 93.8790893555 0.0}
> {-0.0 -0.0 167.392944336}
> TCL: {0.0 0.0 0.0} {459.304840088 0.0 0.0} {-0.0 93.8790893555 0.0}
> {-0.0 -0.0 167.392944336}
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> TOTAL2 TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 2000 24868.6147 123753.2825 54229.5853
> 1209.7959 -2235748.9915 113579.3721 0.0000
> 0.0000 480274.4063 -1437833.9347 310.1541
> -1435275.6421 -1435364.1144 310.1541 34.7683
> 32.3176 7217836.4747 34.7683 32.3176
>
> reading timestep 2000
> TCL: Setting parameter firstTimestep to 2500
> Info: Reading timestep from file.
> Info: Updating unit cell from timestep.
> Info: REMOVING COM VELOCITY -0.00906089 0.00136749 -0.00782743
> TCL: Running for 0 steps
> TCL: {0.0 0.0 0.0} {459.766082764 0.0 0.0} {-0.0 93.8565673828 0.0}
> {-0.0 -0.0 167.408905029}
> TCL: {0.0 0.0 0.0} {459.766082764 0.0 0.0} {-0.0 93.8565673828 0.0}
> {-0.0 -0.0 167.408905029}
> TCL: {0.0 0.0 0.0} {459.766082764 0.0 0.0} {-0.0 93.8565673828 0.0}
> {-0.0 -0.0 167.408905029}
> TCL: {0.0 0.0 0.0} {459.766082764 0.0 0.0} {-0.0 93.8565673828 0.0}
> {-0.0 -0.0 167.408905029}
> ERROR: Constraint failure in RATTLE algorithm for atom 160079!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 339349!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 336289!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely.
> ==========================================
> WallClock: 113.538277 CPUTime: 113.538277 Memory: 662465 kB
> End of program
>
>
> Peter Freddolino wrote:
>> Hi Luca,
>> could you let me know what versions of VMD and NAMD you're using, and
>> what OS? And can I verify your procedure: You loaded your psf and dcd
>> into vmd and then ran namdenergy? How many frames did your dcd have? It
>> looks like there's only one frame of namdenergy output...
>>
>> Peter
>>
>> Luca Bellucci wrote:
>>
>>> Hi all,
>>> I have dcd file named file.dcd for a MD of this kind:
>>> NPT PME with these option dcdfreq 150
>>> xstFreq 150
>>> wrapAll on
>>> dcdUnitCell yes
>>> Then I have this script (arranged by NAMDEnergy VMD script) for
>>> post-analysis:
>>>
>>> \ structure file.psf
>>> \ paraTypeCharmm on
>>> \ parameters par_all27_prot_lipid_na.inp
>>> \ numsteps 1
>>> \ exclude scaled1-4
>>> \ outputname namd-temp
>>> \ temperature 0
>>> \ cutoff 12
>>> \ switchdist 10
>>> \ pairInteraction on
>>> \ pairInteractionGroup1 1
>>> \ pairInteractionFile namd-temp.pdb
>>> \ pairInteractionGroup2 2
>>> \ coordinates namd-temp.pdb
>>> \ run 0
>>> \ set ts 0
>>> \ coorfile open dcd namd-temp.dcd
>>> \ while { ![coorfile read] } {
>>> \ firstTimestep 0
>>> \ run 0
>>> \ incr ts 1
>>> \ }
>>> \ coorfile close
>>>
>>> But the output for energy is wrong. For example:
>>> ELECT VDW 1427.4544 99999999.9999
>>> File namd-temp.dcd generated by
>>> NAMDEnergy script from my original file.dcd. Is this a problem?
>>> Have you any solution?
>>>
>>> Thanks
>>> Luca
>>>
>
>

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