[gmx-users] box size changing during isotropic pressure coupling
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jul 24 13:40:02 CEST 2008
Berk Hess wrote:
> Hmm... this is a (seemingly( really systematic decrease in x and y and
> increase in z.
> But is x at the start really EXACTLY identical to y?
> Because in that case I would think they should always stay identical.
> But looking at the code I see that it is always uses triclinic scaling.
> Thus x and y are treated differently (although adding only zeros),
> so depending on the compiler, the results could differ by a bit.
> What system and compiler are you using?
Pressure coupling artifacts may be enhance by short coupling constants
as well. We recently had a problem that systems consisting of simple
liquids would not equilibrate with tau_p = 1 ps and isotropic scaling.
With tau_p = 5 ps it was fine. For more complicated systems like yours
tau_p might need to be larger. I realize this is somewhat separate from
the issue you are presenting. By the way the website doesn't seem to
> > Date: Fri, 18 Jul 2008 13:54:19 -0400
> > From: chris.neale at utoronto.ca
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] box size changing during isotropic pressure coupling
> > Hello,
> > I have a system of 750,000 atoms consisting of detergent in water.
> > Although this run has been carried out using isotropic pressure
> > coupling, I see significant drift in the box dimensions over 150 ns.
> > This run was carried out using gromacs version 3.3 and 3.3.1. I used the
> > -shuffle and -sort options and an in-house g_desort. This means that my
> > restarts are via grompp, not tpbconv, although I do use the .trr and
> > .edr with gen_vel=no and unconstrained-start=yes for a proper restart.
> > My system is rectangular, starting with an x=y!=z and a=b=c=90. When I
> > view the .xtc file, it is clear that the system is shrinking in the x/y
> > and growing in the z. However, while turning on PBC images it looks like
> > a totally normal simulation in that there is no net drift or anything
> > else obviously problematic.
> > I have posted some images here
> > http://www.pomeslab.com/CN_GromacsPost_071808.html that show the box
> > dimensions over time and also the total volume. The initial rapid volume
> > change, and its asymptotic continuation, is an aggregation effect and is
> > expected. Other than this, the volume is generally stable to the changes
> > in the box lengths along single dimensions. I can not explain any of the
> > features of the individual x/y/z plots, nor can I explain why they level
> > out, why y levels out before x and z, or guess if this will continue to
> > stay (relatively) flat.
> > I am interested to know if anybody else has experienced this. Also, it
> > seems to me like this is simply an output format thing and will not
> > cause problems unless the x/y shrinks so much that cutoff effects cause
> > me problems.
> > my .mdp file follows.
> > title = seriousMD
> > cpp = cpp
> > integrator = md
> > nsteps = 25000
> > tinit = 153200
> > dt = 0.002
> > comm_mode = linear
> > nstcomm = 1
> > comm_grps = System
> > nstxout = 25000
> > nstvout = 25000
> > nstfout = 25000
> > nstlog = 5000
> > nstlist = 10
> > nstenergy = 500
> > nstxtcout = 5000
> > ns_type = grid
> > pbc = xyz
> > coulombtype = PME
> > rcoulomb = 0.9
> > fourierspacing = 0.12
> > pme_order = 4
> > vdwtype = cut-off
> > rvdw_switch = 0
> > rvdw = 1.4
> > rlist = 0.9
> > DispCorr = no
> > Pcoupl = Berendsen
> > pcoupltype = isotropic
> > compressibility = 4.5e-5
> > ref_p = 1.
> > tau_p = 4.0
> > tcoupl = Berendsen
> > tc_grps = DPC SOL
> > tau_t = 0.1 0.1
> > ref_t = 300. 300.
> > annealing = no
> > gen_vel = no
> > unconstrained-start = yes
> > gen_temp = 300.
> > gen_seed = 9896
> > constraints = all-bonds
> > constraint_algorithm= lincs
> > lincs-iter = 1
> > lincs-order = 4
> > ;EOF
> > #########
> > many thanks,
> > Chris.
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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