On Wed, Oct 19, 2016, Saman Yousuf ali wrote:
> Dear All,I have run 70 ps heating step to equilibrate my system before
> moving on to running any production MD simulations. After that, I
> analyzed output of heating steps. I have followed this tutorial for
> plotting http://ambermd.org/tutorials/basic/tutorial3/section6.htm. The
> volume, density and pressure graph of my analysis is weird. I don’t
> understand the reason. I have attached images here.
Please examine the mdout files, and make the plots yourself. Surely the
system volume is not zero at zero time, etc. It is possible that there is
something now wrong with the process_mdout.perl script: this has been
suggested in earlier posts, but I don't remember that anyone has followed up
on that.
...dac
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Received on Wed Oct 19 2016 - 05:00:02 PDT
