Explicit Solvent Sytem (40% Ethanol + 60% Water)

From: Babban Mia (babbanmia_at_gmail.com)
Date: Tue Aug 09 2011 - 01:20:20 CDT

Hello NAMD users

My name is Babban and I have just started to use NAMD and I had been using
CHARMM for a long time before that.

I have following queries regarding an MD simulation that I want to set up ?

1. I want to do a MD in Periodic Boundary Condition for my peptide which is
like 350 amino acids in a combined Ethanol+Water System where Ethanol would
be 40%
Can somebody explain me in good detail about doing that ?

2. Is there way one change/set pH in NAMD ?. I did not find such a thing in
the tutorials?

3. At a pH of 7.4 ,my peptide will have some charge and I would need to put
equivalent charge in my PDB unit cell to neutralize the system?. Those
charges are to be put in local minima.
How do I achieve that?

Please advise.

In anticipation of an encouraigng reply

Best regards

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