From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Fri Mar 10 2017 - 13:34:56 CST
Hello,
While this is a quite ambitious undertaking (lots of computer resources, large noise/error, lipid deformations), you need to make sure the numbers of lipids displaced by the protein is the same between the two end points.
The water is also a challenge as you have noticed. Maybe just expand the box in the z axis to add the water needed to replace the protein volume in the one endpoint.
Brian
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Rabeta Yeasmin
Sent: Friday, March 10, 2017 11:22
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Specify number of water molecules:simulation set up in VMD
Hi,
I am trying to set up TMD simulation for a protein outside the lipid to protein inside the lipid. I have used charmm-gui so far to set up the two system. The problem that I am having is that charmm-gui set up the simulation using different number of water molecules and I did not find any option to specify the number of water molecules. Is there any way in VMD or NAMD to specify the number of water molecules during simulation set up?
Thank you.
Rabeta Yeasmin
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