Samik Bhattacharya wrote:
--- 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
The question is not when energy minimization converged, but whether or not it
converged to an appropriate value of Epot and Fmax. What values did you obtain?
-Justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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