On 2010-09-29 21.15, Ondrej Marsalek wrote:
Hi again,
I have made available a testcase that reproduces the problem here:
http://marge.uochb.cas.cz/~marsalek/tmp/test-volume-drift.tar.bz2
To see the problem, use grompp
from GMX 4.5.1 and run the resulting tpr. Then extract the volume:
echo Volume | g_energy -f ener.edr -o volume
and observe the drift. I would be very grateful if someone could help
me confirm the behavior.
I have found one more thing indicative of this being a bug in 4.5.1.
If I use grompp from 4.0.7 and then run the tpr using 4.5.1 it runs
fine, just as it runs in 4.0.7. The tpr produced by grompp from 4.5.1
has the drift in box volume when run in 4.5.1. Of course, it will not
run in 4.0.7, so there is no way of testing that.
Thanks for any help on this,
Ondrej
I have confirmed this as a bug.
In 4.0.5 (which I had handy) the density is constant
Density (SI) 999.554 3.82377 3.80651 0.0628345 1.25694
In 4.5.1 with 4.0.5 tpr file it is as you say:
Density 995.277 1.3 4.32625 -1.24517 (kg/m^3)
In 4.5.1 with 4.5.1 tpr file I get
Density 709.919 66 137.824 -467.285 (kg/m^3)
Now the differences in the tpr files are revealing:
[anfinsen:test-volume-drift] % gmxcheck -s1 topol405.tpr -s2 topol.tpr
<snip>
Note: tpx file_version 58, software version 73
Reading file topol.tpr, VERSION 4.5.1-%ci-21e8a32 (single precision)
comparing inputrec
inputrec->nstcalcenergy (1 - 10)
inputrec->rgbradii (2.000000e+00 - 1.000000e+00)
inputrec->sa_surface_tension (2.092000e+00 - 2.050160e+00)
inputrec->sc_sigma_min (0.000000e+00 - 3.000000e-01)
inputrec->nstdhdl (1 - 10)
inputrec->separate_dhdl_file (0 - 10)
<snip>
After setting nstcalcenergy = 1 I get
Density 996.894 1.2 3.85083 1.86718 (kg/m^3)
In other words the bug can be circumvented by setting this variable to
1. I will file a bugzilla.
On Thu, Sep 23, 2010 at 15:16, Ondrej Marsalek
<ondrej.marsa...@gmail.com> wrote:
Dear all,
running a box of neat water with the below mdp file in GROMACS 4.5.1
results in a fast linear increase of the volume of the box, the water
getting torn into clusters. The same simulation in 4.0.7 (with
nstcalcenergy removed, of course) runs just fine, with the box volume
stable and fluctuating. In 4.5.1 the problem can be fixed by setting
nstlist = 1. I assume this would also be the case for other positive
numbers. The same behavior can be seen for the Parrinello-Rahman
barostat. I can of course provide full testcases ready to run, if
needed.
This looks like a bug to me. Can anyone help me resolve this?
Thanks,
Ondrej
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0
dt = 0.002
nsteps = 5000
comm-mode = Linear
nstcomm = 10
; OUTPUT CONTROL OPTIONS
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 100
nstcalcenergy = 10
nstenergy = 100
nstxtcout = 100
xtc-precision = 1000
; NEIGHBORSEARCHING PARAMETERS
nstlist = -1
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 1.3
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME-Switch
rcoulomb-switch = 0.6
rcoulomb = 0.8
vdw-type = Shift
rvdw-switch = 0.6
rvdw = 0.8
DispCorr = EnerPres
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS
Tcoupl = v-rescale
tc-grps = system
tau_t = 0.5
ref_t = 300
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1
compressibility = 4.5e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
; OPTIONS FOR BONDS
constraints = none
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
