On 2/14/18 1:06 PM, kordza...@aut.ac.ir wrote:
Hi Dr.Lemkul

Thank you very much for your answer

I get it now, before your answer I run system with -maxwarn 1, I saw trajectory 
in vmd , my drug molecule break in middle of run and then corrected, is it 

No, that's called periodic boundary conditions.

has it occured because using maxwran?


is vmd an appropriate tool for detect trajectory?

You can use whatever visualization software you like, but you should use trjconv first to get a consistent, intact representation.

I alaways after run, check trajectory with vmd to sure in time of simulation 
all structure were complete.

VMD is good for visualizing and some analysis, but it's not going to tell you anything about the physical validity of your simulation or the methods you used. That's what grompp was warning you about in the first place. If the simulation finished, there was likely no problem; the warning is intended to tell you that things *may* be unstable with Parrinello-Rahman if you are simultaneously generating velocities.

I will do your advise, and I will run with Benedsen probably it will solve my 

The "broken" molecule is not a problem and will not be magically solved by using a different barostat.



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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