[gmx-users] distance restraints in mdp

Justin Lemkul jalemkul at vt.edu
Wed Mar 9 02:35:09 CET 2016

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On 3/8/16 8:19 PM, Sana Saeed wrote:
> dear Justin Lemkuli already run that without restraints, it has no problems.
> even i used the gro file from the simple 5ns MD but still have these same
> errors and warnings. when i set Lincs constraints to all-bonds , simulation
> finishes fine but by using alchemical_analysis.py for free energies it gives
> errors and warnings. (Warning: states 29 and 37 have the same energies on the
> dataset.) i used 42 lambdas and about 32 states are having same energies. and
> when i set constraints to h-bonds then LINCS warnings. i tried to use
> different options for pressure coupling also because i read somewhere it also
> affects simulation. i am quite confused where the problem is. is it possible
> to send you topology file and you have a look?Thanks in advance

Now we're talking about half a million different things.  When reporting a 
problem, please keep it simple.  It's impossible for anyone on this mailing list 
to be inside your head and know what you've done.

If you want to troubleshoot distance restraints, we can do that.  But let's take 
things one at a time.  If you want to share files, please upload a tarball of 
*all* input files: coordinates, topology(ies), any relevant .mdp file(s), and a 
run script that lists all of your commands, exactly in sequence as you typed 
them.  Please do not send this information privately; share with the list so 
others can contribute (I'm frankly swamped lately and have little time to delve 
deeply into such issues but I'll try to make a little time).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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