--- On Wed, 15/7/09, Mark Abraham <mark.abra...@anu.edu.au> wrote:
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Lincs Warning
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Date: Wednesday, 15 July, 2009, 5:23 PM
Samik Bhattacharya wrote:
> Hi all, i ma simulating a membrane protein, in which i am facing a problem in
> the equilibration step. in the NVT equilibration when i am running the mdrun
> command i am getting a msg like
>
> Program mdrun, VERSION 4.0.5
> Source code file: constr.c, line: 136
>
> Fatal error:
> Too many LINCS warnings (1966)
> If you know what you are doing you can adjust the lincs warning threshold in
> your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> i cant understand how to fix the problem. where actually lies the error? is
>it in the mdp file i am using? some suggestions will be really helpful in this
>regard. Thank you all for the help in advance.
http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
Thanks You Mark. for your help... perhaps the error lies lies in EM step which
converged very early in previous steps. when i was running EM for 5000 steps it
was converging in less than 50 steps. and was showing a msg like
Stepsize too small, or no change in energy. Converged to machine precision, but
not to the requested precision
would doule precision remove this problem? again i cant rule out the system
blowing up error. in that case how to increase 1-4 interaction?
looking forward for your valuable comments. Thank You
Shamik
Yahoo! recommends that you upgrade to the new and safer Internet Explorer
8. http://downloads.yahoo.com/in/internetexplorer/_______________________________________________
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
