[gmx-users] LINCS WARNING - Protein-Membrane-system

Justin Lemkul jalemkul at vt.edu
Tue Jan 1 16:47:22 CET 2013

On 1/1/13 10:41 AM, Shima Arasteh wrote:
> Thanks.
> I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was  "constraints  = h-bonds ", however it was "constraints = all-bonds" for POPC/PROTEIN/WATER system.
> You say insufficient minimization, I don't think so........ . I got a sensible potential energy as follow:
> Potential Energy  = -1.2414742e+06
> Maximum force     =  9.8055229e+01 on atom 4719
> Norm of force     =  3.4904923e+00
> Then what's wrong with the EM?

Please post a complete .mdp file for both the EM and NVT processes.  Without 
that information, it's pure guesswork.



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


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