VMD-L Mailing List

From: Babban Mia (babbanmia_at_gmail.com)
Date: Tue Aug 09 2011 - 04:16:03 CDT

Hello VMD users

I want to do an explicit solvent MD in NAMD . Explicit Solvent would be 40%
Ethanol and 60% Water but before that I must be able to set up a proper
explicit system. I read that it is quite easy to solvate a protein in vmd
,even with the custom solvent.

I will be grateful if someone could tell me the step by step procedure to
achieve the set up of my explicit system.

I guess I would just need the PDB and PSF file of the final system (i.e
protein+ 40% Ethanol+60% Water Solvent ) which then can be loaded onto NAMD
for Molecular dynamics.

Any help would be great .or if anybody knows another way of doing it.

Best Regards
Babban