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

[Justin A. Lemkul]

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

-- 
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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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