VMD-L Mailing List

From: James Kress (jimkress_58_at_kressworks.org)
Date: Mon Oct 07 2019 - 10:06:23 CDT

If periodic boundary conditions are imposed, why is there any need to have the protein centered in the box during the course of the MD run?

 

When the run in complete I can see the need to wrap to center the protein. Otherwise, it is always effectively at the center.

 

Jim

 

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From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> On Behalf Of Adupa Vasista
Sent: Monday, October 07, 2019 3:27 AM
To: Santhosh Ranga <santhoshchemistry528_at_gmail.com>
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: query on how to allow the protein to interact with the water molecules

 

Hi,

Your protein can't be in the center of the box every time, it can move freely around . if you want your protein to be in the center of the box, I suggest you do wrapping after a run by the following command

 

"pbc wrap -all -compound fragment -center com -centersel protein "

 

https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/#x1-180006 I suggest you read this for more information.

 

 

On Mon, Oct 7, 2019 at 10:49 AM Santhosh Ranga <santhoshchemistry528_at_gmail.com <mailto:santhoshchemistry528_at_gmail.com> > wrote:

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.

 

 

On Mon, Oct 7, 2019 at 10:49 AM Santhosh Ranga <santhoshchemistry528_at_gmail.com <mailto:santhoshchemistry528_at_gmail.com> > wrote:

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.

  

-- 
A.Vasista
M.Tech,Department Of Chemical Engineering,
IIT Guwahati.