[gmx-users] Re: Regarding error in equilibration step

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 22 13:03:33 CET 2010

Please keep all Gromacs-related correspondence on the gmx-users list.  I do not 
advertise myself as a private tutor, and furthermore, archived discussions serve 
the community as the whole.  I am CC'ing the list in my reply; please continue 
the discussion there.

Jignesh Patel wrote:
> Respected Sir,
>                      I am trying to do membrane protein dynamics as per 
> VERGINIA TECH tutorial. After energy minimization I got energy within 
> the range but Fmax is greater than 1000. Further i am trying to perform 
> equilibration with same .gro file which is generated by energy 
> minimization. But here I am getting LINCS error.

Sure, if you plow ahead after incomplete or unsatisfactory energy minimization, 
you should certainly expect that the system is unstable and will crash.

> Can you suggest me how to overcome this problem?

At the end of EM, mdrun prints out the atom on which the maximum force is 
acting.  Look and see what that atom is (in VMD, PyMol, etc) and figure out why 
such a large force is acting there.  Perhaps you have over-compressed the system 
with InflateGRO, or otherwise not followed some other earlier part of the tutorial.


> Thanking you in anticipation.                   
> -- 
> Research Scholar,
> National Institute of Pharmaceutical Education and Research (NIPER),
> Mohali,
> India.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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