On 2/12/18 6:34 AM, kordza...@aut.ac.ir wrote:
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
Justin A. Lemkul, Ph.D.
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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