On 2/12/18 6:34 AM, kordza...@aut.ac.ir wrote:
Hi Dr.Abraham

Thank you very much for your answer

yas I 've extacted configuration with 0.2 nm distance and when I want to 
run NPT for first configuration,I gave that error.

I didn't undersatnd this mdp file for this step, I got this file from umbrella 
sampling tutorial and I adjusted for my system but I didn't understand

we are doing a pullind simulation with zero velocity, I think the aim is to 
costriant structure by artifial spring but we don't  move it, am I right?

The application of a biasing potential (which is not a constraint) is separate from the technical issue of Parrinello-Rahman pressure coupling being applied in conjunction with generating velocities. I wrote the tutorial and input files years ago when grompp didn't complain about this. I had no problems with stability, but this may not always be the case. So grompp is trying to help you by pointing out that this particular combination of options may not be wise. You may wish to do a short NPT equilibration with Berendsen pressure coupling before starting data collection.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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