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Hi,<br>
<br>
Can you also post your .mdp?<br>
<br>
Ran<br>
<br>
Berk Hess wrote:
<blockquote cite="midCOL113-W61DA6B32B20C13A095E1EE8E380@phx.gbl"
type="cite">
<style><!--
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--></style>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: <a class="moz-txt-link-abbreviated" href="mailto:schlesi@uni-mainz.de">schlesi@uni-mainz.de</a><br>
> To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><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>
> > <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> > Please search the archive at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a>
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
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>
> -- <br>
> gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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> Please search the archive at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before
posting!<br>
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