[gmx-users] reg lincs error and exploding problem during mdrun

Justin A. Lemkul jalemkul at vt.edu
Mon May 2 12:49:25 CEST 2011

vidhya sankar wrote:
> Thanks Justin,
>                       now i have different problem when i run mdrun_d 
> programme with the following command
>  ./mdrun_d -s 1HHO_md.tpr -o 1HHO_md.trr  -c 1HHO_md.gro -e md.edr -nt 1
> i got error as follows
> Step 0, time 0 (ps)  LINCS WARNING

LINCS warnings that occur immediately are almost invariably the result of a poor 
starting configuration.  Better energy minimization and/or equilibration are 
likely necessary.

Another consideration is whether or not these groups:

> tc-grps     =  HEM   AL    OXY    ; two coupling groups - more accurate

are large enough to justify setting them separately.  Small groups can be 
unstable by themselves.  Hence why one does not, for example, couple ions 
separately from solvent.



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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