Re: Re:

From: Jim Phillips (
Date: Wed Apr 13 2011 - 10:19:45 CDT

This is my guess too. You probably didn't use extendedSystem to load the
.xsc file from the end of the NPT simulation and you've gone back to the
original periodic cell specified in the config file.


On Mon, 11 Apr 2011, Erik Nordgren wrote:

> 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 <>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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