On 1/1/13 10:41 AM, Shima Arasteh wrote:
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 

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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