From: Axel Kohlmeyer (
Date: Sat Jun 29 2013 - 02:06:10 CDT

You can load the files into vmd and use a selection when saving them. But this can only work if you remove items that are not bound to the rest. For more sophisticated operations you need to use scripting and the topotools plugin.

That being said, you won't save much time, because you cut a hole into your system, which will lead to an implosion and a nasty little sound wave, that will keep running through your system due to PBC and that you need to equilibrate away just as when you start from scratch.

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

-----Original Message-----
From: Peterson J <>
Date: Fri, 28 Jun 2013 22:06:56
To: <><>
Subject: vmd-l: Reusing the psf file

Hi Everyone.

I have problem re-simulating my system from my previous simulation.
Actually I want to remove a set of residues from my protein part and use
the same psf to continue running the simulation since I dont want to spend
long time on equilbrating the system once again.

I tried many ways but since the atom numbers are different I couldn't use
the same old psf files. I also divided all my segments and generating the
psfs for all segments and try putting them together but the water and lipid
molecules (which are added as various segments) have problem because of
their same residue numbers with the protein.

Any solution to this?