[gmx-users] box size changing during isotropic pressure coupling
gmx3 at hotmail.com
Thu Jul 24 17:11:10 CEST 2008
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.
> 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.
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > Express yourself instantly with MSN Messenger! MSN Messenger
> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
> > ------------------------------------------------------------------------
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users