[gmx-users] Turn-off water optimisation

[Berk Hess]

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: 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 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 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
 		 	   		  
_________________________________________________________________
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...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100305/26edf54d/attachment.html>