[gmx-users] linc warnings

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 30 13:16:53 CET 2009

Justin A. Lemkul wrote:


>> were harmonically restrained to their initial positions of pdb, How 
>> can I do this for my fe4s4 cluster. What keywords should I use for 
>> that  and in which step I can do?
> That's what position restraints are doing.

I should amend this slightly.  I assumed your Fe4S4 cluster was simply part of 
your protein, which is restrained with posre.itp, generated by pdb2gmx.  If this 
is not the case, you will have to use genrestr to generate a position restraint 
file for the Fe4S4 cluster, if it is indeed a separate molecule type.

I doubt that restraining the Fe4S4 cluster will fix anything.  Please see my 
last message - there are clashes in your system or inappropriate parameters at 
play.  If you restrain the atoms, you may be just delaying the inevitable crash.



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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