VMD-L Mailing List

From: Santhosh Ranga (santhoshchemistry528_at_gmail.com)
Date: Sun Oct 06 2019 - 23:45:36 CDT

Dear Team_at_NAMD,

I am Dr. Santosh Ranga, a postdoctoral fellow, in the department of
chemistry, the Indian Institute of Technology (IIT B), Mumbai.

I was trying to perform initial MD simulations systematically using NAMD.
My query is that I want to allow the protein to interact with the solvent
(water), but at the same time, it should be at the center of the box.

fixedAtoms on

fixedAtomsFile myfixedatoms.pdb ;# flags are in this file

fixedAtomsCol B ;# set beta non-zero to fix an atom

When I include these keywords in the conf file, my protein is frozen in the
center, not given flexibility.

My idea is that I want to give the flexibility for both solute and the
solvent being protein at the center.

Please help me what the changes I have to do in the PDB file or conf file
so that I would be able to see what is happening with time are.

Since I am new to MD simulations using NAMD, educate me with your
knowledge.

I appreciate your patience.

Thank you,

IPDF, IIT Bombay,

India.