[gmx-users] com motion

Mustafa Toprakçý denn22 at excite.com
Wed Apr 9 13:29:01 CEST 2003

Hi Christoph,
Sorry for the delay. I was in lecture. Well I am using vacuum simulation
and fixing protein to its coordinates and only making ligand free..
Maybe I am misinterpreting the run parameters. I have used 

nstcomm = 0
comm_mode = none
comm_grps = ---
freezegrps = protein
freezedim = Y Y Y

I have checked the mdout.mdp produced by grompp and it does not show
any definiton of comm group for system. 
Comm_mode = none should remove all the restriction on this motion.
I have fixed the protein. So there stays only the ligand comm to move.
I have also tested with comm_grps = protein but this did not differ too. I did not checked with MSD yet.


 --- On Wed 04/09, Christoph Freudenberger < christoph.freudenberger at chemie.uni-ulm.de > wrote:
From: Christoph Freudenberger [mailto: christoph.freudenberger at chemie.uni-ulm.de]
To: gmx-users at gromacs.org
Date: Wed, 09 Apr 2003 11:43:34 +0200
Subject: Re: [gmx-users] com motion

Mustafa ToprakXX wrote:<br>> Ok David,<br>> The temperature is what I want. According to my understanding the <br>> update algorithm corrects the VCM and prevents accumulation of kinetic<br>> energy in the center of mass. When I checked the com xvg file this is<br>> clearly seen. Just like the temperature, the com koordinates does not <br>> change much.<br>>   so it seems the code does not sample such kind of motion efficiently.<br>> Such a simulation may be sampled under external forces but that would<br>> be too unrealistic. Because it would be better to sample under intermolecular forces.<br><br>I don't really understand, what you accually want to do...<br>You're studing a ligand that is docked to some receptor protein and<br>want to see how much the ligand moves around the protein. is that<br>correct?<br>Are you doing this in vakuum or in a solvent? if do which one<br>and why is there no temp coupling for it in the mdp?<br><br>Concerning the COM motion: I gather from the 
 mdp that you<br>keep the protein coords frozen. You have not defined a COMM group so<br>I suppose the COMM is computes for the whole system and (as the<br>mass of the protein is surely some orders of magnitude larger than<br>that of the ligand) the ligand motion is maybe just averaged out.<br>Did you check the protein ligand distance by MSD?<br><br>-- <br>Christoph Freudenberger<br>Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785<br><br>_______________________________________________<br>gmx-users mailing list<br>gmx-users at gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request at gromacs.org.<br>

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