[gmx-users] Re: NPT MD Run Problem

[Justin A. Lemkul]

teklebrh at ualberta.ca wrote:
> Dear Gromacs users,
> 
> I have equilibration my system using the position restraint NVT 
> simulation for 100ps, and it works well. and did not get any error until 
> the end.
> 
> But as soon as I switch to NPT full production run, I got the following 
> error. Can any body help me on this issue.
> 
> Program mdrun, VERSION 4.0.5
> Source code file: constr.c, line: 136
> 
> Fatal error:
> Too many LINCS warnings (6540)
> 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

> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen-vel                  = yes ; assign velocities from Maxwell 

Re-generating velocities negates the purpose of any previous equilibration.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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