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

[David van der Spoel]

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