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