[gmx-users] Turn-off water optimisation
r.friedman at bioc.uzh.ch
Fri Mar 5 15:04:43 CET 2010
Can you also post your .mdp?
Berk Hess wrote:
> I have never heard about problems like this before.
> It seems highly unlikely to me that the innerloops are causing this.
> Are your running exacly the same tpr file on your local machine
> and the cluster?
> You probably want to update to version 4.0.7 to be sure you have
> all the latest bugfixes.
> Please keep us updated on this issue, since things like this should
> never happen (unless there is a compiler bug).
> > Date: Fri, 5 Mar 2010 14:41:02 +0100
> > From: schlesi at uni-mainz.de
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Turn-off water optimisation
> > Hi,
> > i have the following problem: (GROMACS 4.0.5)
> > when i simulated water in serial on our cluster with the brendsen or
> > v-rescale thermostat i get to high temperatures (300 K goes in very
> > short time up to around 425 K). If i simulate in parallel or at my
> > machine i get no problems. Also if i change water to another molecule
> > there are no such problems. (I use the same mdp file for all the
> > simulations).
> > Because the problem appears with water (spc and tip4p) but not with
> > mesitylene i thought probably the special things for water (settle, and
> > so on) could be the problem. So i wanted to simulate water without that
> > fancy stuff.
> > Thanks for the info with the enviroment variable, but where can i
> set it?
> > For the other problems (why it works on the cluster in parallel, but
> > in serial, but works on the local-pc in serial) i have so far no idea,
> > where to look. But first i'm happy to know if the problem comes from
> > special water-loops.
> > Thomas
> > >Hi,
> > >
> > >You don't want to mess with the topology, you will be simulating a
> > quit >different
> > >system when you turn off constraints. Also Gromacs does not optimize
> > >based
> > >on names, since the name might not say anything about the molecule.
> > >I don't know what effect of what optimizations you want to test,
> > >but setting the environment variable GMX_NO_SOLV_OPT will turn off
> > >the special inner-loops for water.
> > >
> > >Berk
> > > Date: Fri, 5 Mar 2010 11:31:50 +0100
> > > From: schlesi at uni-mainz.de
> > > To: gmx-users at gromacs.org
> > > Subject: [gmx-users] Turn-off water optimisation
> > >
> > > Dear all,
> > > I simulated water (spc) with the ffG53a5 force field. For testing
> > > propose i want to turn of the water optimisation. How do i do this?
> > > So far i have tried:
> > > * contraints = none
> > > * define = -DFLEXIBLE
> > > * took the spc.itp file and deleted all the stuff for settle and the
> > > other force fields, changed resname from SOL to WAT (also spc.itp ->
> > > wat.itp)
> > >
> > > But all the time i the log file there is this line:
> > > Enabling SPC water optimization for 1184 molecules.
> > >
> > > Espically with the last option (change of the spc.itp) i don't how
> > > GROMACS recorgnises that i simulate SPC water, because i has a
> > > name and so.
> > >
> > > Thanks for your help in advance.
> > > Greetings
> > > Thomas
> > > --
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://lists.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
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > 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
> New Windows 7: Simplify what you do everyday. Find the right PC for
> you. <http://windows.microsoft.com/shop>
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users