From: Daniela Rivas (dani.rivas.r_at_gmail.com)
Date: Thu Mar 31 2016 - 11:21:03 CDT
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--001a1140c5781cfd2d052f5aa652--
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