[gmx-users] box size changing during isotropic pressure coupling

Berk Hess gmx3 at hotmail.com
Thu Jul 24 17:11:10 CEST 2008 

Hi,

Here tau_p=4, which is already quite large.
But there are no "real" problems in the system, the results should be fine.
But the relative ling tau_p might be the reason for the strange scaling.
This would make the scaling factor always close to 1 plus or minus one bit.
I have not done the binary math, so I can not see if somehow this would
make numbers slightly below 20 scale down and above 20 scale up.

Berk.


> Date: Thu, 24 Jul 2008 13:40:02 +0200
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] box size changing during isotropic pressure coupling
> 
> Berk Hess wrote:
> > 
> > Hi,
> > 
> > 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 
> exist anymore.
> 
> > Berk.
> > 
> > 
> >  > 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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