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: [EMAIL PROTECTED]
> To: [email protected]
> 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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