Re: vmd-l: query on how to allow the protein to interact with the water molecules

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Oct 08 2019 - 09:01:51 CDT

Dear Santosh,

 

This thread should be in the namd-l, and not vmd-l. I am moving the conversation to the namd-l, and I would ask you to keep the namd-l in your answers, but not vmd-l.

 

What you are looking for is to add a harmonic restraint to your protein https://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html. Please take a look at the “constraints” section of the link that I sent.

 

There is also some explanation in a previous namd-l thread - https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/0751.html and here https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2003-2004/0136.html

 

 

Best,

 

João

 

 

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Santhosh Ranga <santhoshchemistry528_at_gmail.com>
Date: Sunday, October 6, 2019 at 11:45 PM
To: <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: query on how to allow the protein to interact with the water molecules

 

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.

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