From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Mon Apr 11 2011 - 21:38:33 CDT
Hi Maiti,
You haven't given your fellow NAMD users much information to go on here in
order to help you. Perhaps if you sent us a copy of your NAMD config
scripts (one with NPT and the later one using NVT) that would be a good
start.
The first thing that occurs to me is that you might have specified an
incorrect box size for your NVT run; perhaps you used the initial system
size (from before it was changed by your long constant-volume run) by
mistake? What were the dimensions of your MD box before and after your NVT
run? (This info will be in your *.xst output file.)
regards,
Erik
-- C. Erik Nordgren, Ph.D. Chemistry Department University of Pennsylvania On Mon, Apr 11, 2011 at 3:27 PM, Buddhadev Maiti <chebm_at_langate.gsu.edu>wrote: > Dear NAMD Users, > I am working on membrane simulation. I did long NPT run to compress the box > and no undesirable gaps present between the periodic images of box. After > that I switch to NPT ConstantArea production run. I am getting immediately > gaps between the periodic images basically in corner. And also the gaps are > in between protein and lipids. If I go for more production run, the gaps are > growing more and I am getting unphysical results. Could you please reply me > any suggestions, it will be great help for me. > Have a nice day, > Thanks, > Maiti > >
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