From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Fri Apr 01 2016 - 12:09:44 CDT
Dear Daniela,
The density at the start of your second run is expected to be different than that of your first run, due to running a constant pressure simulation that has the effect of resizing space.
Is the jump in volume evident on the very first step when you continue, or soon after you continue? You should be able to verify by looking at the log file from your second run that the cell basis vectors are getting set correctly from your XSC file.
I think that when you restart you need to set “COMmotion=yes” so that the velocities are not altered to remove the center of mass motion. (Can someone who routinely does simulation work with NAMD please verify?) This could account for the jump in energy.
Two other points:
1. You have made a poor choice for the PME grid sizes. When setting the grid sizes, always choose something that is a power of 2 if possible, or a power of 2 times a small odd prime number. For instance, you would be better off choosing 192 for the longer dimensions and 128 for the shorter dimension.
2. I had thought that the use of fixed atoms was incompatible with constant pressure, since in a constant pressure simulation, space is being resized and the atom positions are rescaled by the same factor that is changing the simulation cell.
Best regards,
Dave
--
David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
dhardy_at_ks.uiuc.edu
http://www.ks.uiuc.edu/~dhardy/
> On Mar 31, 2016, at 11:21 AM, Daniela Rivas <dani.rivas.r_at_gmail.com> wrote:
>
> Thanks to all of you!
> Unfortunately I don't think that's the issue here, because on my first run
> I used the same frequency (500) for restart and dcd files. I knew I had to
> stop my simulation, because we were going to move the lab to another
> building, so I used the same frequency for all files. Then, when we finally
> moved, I changed the restart frequency because the simulation wouldn't be
> stopped anymore.
> Now, these are the last lines from my first run in the log file:
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 28762500
> WRITING COORDINATES TO DCD FILE dinamica_modelo.dcd AT STEP 28762500
> WRITING COORDINATES TO RESTART FILE AT STEP 28762500
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 28762500
> FINISHED WRITING RESTART VELOCITIES
> TIMING: 28763000 CPU: 1.78773e+06, 0.064571/step Wall: 1.78773e+06,
> 0.064571/step, 1277.93 hours remaining, 836.468750 MB of memory in use.
> ENERGY: 28763000 77417.8685 81138.1303 20717.3272
> 516.9516 -775319.5863 45253.4701 0.0000 0.0000
> 228438.5374 -321837.3012 308.4605 -550275.8386
> -318861.0936 309.2387 2194.0153 165.2460
> 2376703.0655 -8.1043 -8.5127
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 28763000
> WRITING COORDINATES TO DCD FILE dinamica_modelo.dcd AT STEP 28763000
> WRITING COORDINATES TO RESTART FILE AT STEP 28763000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 28763000
> FINISHED WRITING RESTART VELOCITIES
>
> And these are the first ones (when saving data on the dcd file) from the
> second run in the log file:
>
> TIMING: 28763500 CPU: 21.234, 0.0418484/step Wall: 21.234,
> 0.0418484/step, 1162.45 hours remaining, 603.437500 MB of memory in use.
> ENERGY: 28763500 78685.2312 84533.7344 21013.8176
> 536.5008 -831141.8348 49193.2087 0.0000 0.0000
> 230851.0850 -366328.2571 311.7181 -597179.3422
> -363275.0546 313.1683 2806.6282 81.8951
> 2358682.9921 4.1570 4.2652
>
> OPENING COORDINATE DCD FILE
> WRITING COORDINATES TO DCD FILE dinamica_modelo2.dcd AT STEP 28763500
> The last position output (seq=28763500) takes 0.042 seconds, 603.438 MB of
> memory in use
> Info: Benchmark time: 12 CPUs 0.040986 s/step 0.474375 days/ns 609.332 MB
> memory
> Info: Benchmark time: 12 CPUs 0.0405642 s/step 0.469492 days/ns 609.766 MB
> memory
> Info: Benchmark time: 12 CPUs 0.0405513 s/step 0.469343 days/ns 610.195 MB
> memory
> Info: Benchmark time: 12 CPUs 0.0406136 s/step 0.470065 days/ns 610.309 MB
> memory
> TIMING: 28764000 CPU: 41.6428, 0.0408176/step Wall: 41.6428,
> 0.0408176/step, 1133.81 hours remaining, 610.718750 MB of memory in use.
> ENERGY: 28764000 79263.5695 84579.6372 20907.3695
> 519.1135 -835175.1423 48799.6018 0.0000 0.0000
> 229636.5280 -371469.3227 310.0781 -601105.8507
> -368374.2038 311.4156 2413.3487 61.1194
> 2351873.5970 -3.7612 -3.5247
>
> Finally, this is the conf file I used on my first run:
>
> # INPUT FILES #
>
> structure Modelo23_memb_ion.psf
> coordinates Modelo23_memb_ion.pdb
>
> # Starting from scratch #
>
> temperature 0
>
> # Continuing a job from the restart files #
>
> if {0} {
> set inputname dinamica_modelo ;# only need to edit this
> in one place!
> binCoordinates $inputname.coor ;# coordinates from last
> run (binary)
> binVelocities $inputname.vel ;# velocities from
> last run (binary)
> extendedSystem $inputname.xsc ;# cell dimensions from last run
> firsttimestep 1 ;# last
> step of previous run
> numsteps 100000000 ;# run stops when
> this step is reached
> }
>
> # OUTPUT FILES #
>
> binaryoutput off
> outputname dinamica_modelo ;# dinamica_modelo2 if restart!
> outputEnergies 500
> outputTiming 500
> restartfreq 500
> xstFreq 500
> dcdFreq 500
> wrapAll on
> wrapNearest on
>
> # FORCE-FIELD PARAMETERS #
>
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
>
> # PARAMETERS #
>
> firsttimestep 0
> timestep 1
> nonBondedFreq 2
> fullElectFrequency 4
> stepsPerCycle 20
>
> switching on
> switchDist 8.5
> cutoff 10
> pairlistdist 11.5
>
> exclude scaled1-4
> 1-4scaling 1.0
>
> # SYSTEM BOUNDARY CONDITIONS #
>
> cellBasisVector1 153.00 00.00 00.00
> cellBasisVector2 00.00 153.00 00.00
> cellBasisVector3 00.00 00.00 114.00
> cellOrigin 30.61 08.79 04.27
> margin 5
>
> Pme on
> PmeGridsizeX 158
> PmeGridsizeY 158
> PmeGridsizeZ 119
>
> # FIXED ATOMS #
>
> fixedAtoms on
> fixedAtomsForces off
> fixedAtomsFile myfixedatoms.pdb
> fixedAtomsCol B
>
> # CONSTRAINTS #
>
> #constraints off
> #consRef off
> #consKFile off
> #consKCol off
>
> # PRESSURE AND TEMPERATURE CONTROL #
>
> langevin on
> langevinDamping 10
> langevinTemp 310
> langevinHydrogen no
>
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 200
> langevinPistonDecay 100
> langevinPistonTemp 310
>
> useGroupPressure yes # smaller fluctuations
> useFlexibleCell yes # allow dimensions to fluctuate independently
> useConstantRatio yes # fix shape in x-y plane
>
> # DYNAMICS #
>
> # run one step to get into scripting mode
> minimize 0 ;# comment if restart
>
> # turn off until later
> langevinPiston off ;# comment if restart
>
> # minimize nonbackbone atoms
> minimize 10000 ;# comment if restart
> output min_fix2 ;# comment if restart
>
> # min all atoms
> #fixedAtoms off
> minimize 1000 ;# comment if restart
> output Modelo23_min ;# comment if restart
>
> # heat with CAs restrained
> # langevin on
> #run 10000
> #output heat2
>
> # equilibrate volume with CAs restrained
> langevinPiston on
> run 100000000
> output Modelo_final
>
> # equilibrate volume without restraints
> # constraintScaling 0
> # run 10000
>
> Finally, I noticed that this changed in the second run:
>
> First run:
> Info: MASS DENSITY = 1.03483 g/cm^3
> Info: ATOM DENSITY = 0.104538 atoms/A^3
>
> Second run:
> Info: MASS DENSITY = 0.921625 g/cm^3
> Info: ATOM DENSITY = 0.0931026 atoms/A^3
>
> So, there was a change in the mass and atom density. Can this be the reason
> of the jump? Why could this happen? Is this normal?
>
> Thanks a lot for your help!
>
> Kind regards,
> Daniela.
>
>
> On Thu, Mar 31, 2016 at 11:13 AM, Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> Ahhh, I third that explanation. I hadn’t looked closely enough at the stem
>> of your inputname — I thought you were using the coor/vel/xsc files written
>> at the end of the run, but missed the fact that you were actually using the
>> .restart.* files because that was defined in inputname
>>
>>> On Mar 31, 2016, at 9:44 AM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
>>>
>>> Dear D
>>>
>>> I second Norman Geist. This is likely the issue:
>>>
>>> outputEnergies 500
>>> restartfreq 1000000
>>>
>>> The firsttimestep seems to suggest that the last energy was written at
>> 28763000 steps. But, the last restart files were written at step 28000000
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