Hi, Can you also post your .mdp?
Ran Berk Hess wrote: > Hi, > > 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). > > Berk > > > Date: Fri, 5 Mar 2010 14:41:02 +0100 > > From: schl...@uni-mainz.de > > To: gmx-users@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 > local > > 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 > not > > 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 > the > > 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 > different > > > 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@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-requ...@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>
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