[gmx-users] com motion

[Mustafa Toprakçý]

Hi David,
That's ok. I apply this as you say. Could I ask it another way? here 
are two top files

1st type top file

[ system ] 

Ligand-protein complex 

[ molecules ] 

Complex  1



2nd type top file

[ system ] 

Ligand-protein complex 

[ molecules ] 

Protein  1
Ligand   1

In both simulations I define protein part in freezegrp and ligand as
free com group and give separate temperatures. Does these two top 
files make different meanings to the program to sample ligand com
motion. Or which one is better for this kind of simulation?

Thanks
Mustafa




 --- On Fri 04/04, David van der Spoel < spoel at xray.bmc.uu.se > wrote:
From: David van der Spoel [mailto: spoel at xray.bmc.uu.se]
To: gmx-users at gromacs.org
Date: 04 Apr 2003 11:54:55 +0200
Subject: Re: [gmx-users] com motion

On Fri, 2003-04-04 at 11:14, Mustafa Toprakçý wrote:<br>> <br>>  Dear Gromacs Team,<br>> I would like to ask one issue. I have defined a substrate-enzyme<br>> complex system, using pdb2gmx as 1 molecule in the .top file. I might<br>> have also defined the same system as 2 molecules such as protein and<br>> ligand in the .top file.<br>> I am simülating center of mass motion, Does it differ for the program<br>> to see the system as one or two molecules in the aspect of ligand center<br>> of mass simülation?<br><br>All groups must be mutually exclusive, that is for COM an atom can only<br>be in one group, same for energies. However, energy groups and COM<br>groups must not be the same, they can, but it's not necessary.<br>> <br>> Thanks<br>> Mustafa<br>> <br>> <br>> <br>> <br>> _______________________________________________<br>> Join Excite! - http://www.excite.com<br>> The most personalized portal on the Web!<br>> _______________________________________________<br>> gmx-users 
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