[gmx-users] co-solvent simulation

Yao Yao yao0o at ymail.com
Sun Feb 12 08:06:56 CET 2012

Actually even I follow the ""http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents"and try the built-in ureaas co-solvent, 

it has the same problem (solvate urea as protein can work, but does not work if you consider it as co-solvent).
I do not know if anyone has met the same problem before.



----- Forwarded Message -----
From: Yao Yao <yao0o at ymail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, February 11, 2012 10:47 PM
Subject: Re: [gmx-users] co-solvent simulation

Hi Mark,

Thanks for your reply. I have not figured out what the problem. BUt I am thinking if I have two proteins in my system, 

like simulating the protein-protein interaction, what I should call the second protein for [moleculetype] in my .top, still "protein"?



 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, February 11, 2012 9:39 PM
Subject: Re: [gmx-users] co-solvent simulation

On 12/02/2012 4:16 PM, Yao Yao wrote: 
I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents".
>Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp
You should not need to touch this file to model glycerol. There are
    no atom or interaction types that are materially different from
    those on peptide side chains.

and aminoacids.rtp.
>For test purpose, I then made a itp for it and solvate it as a protein and changed .top file accordingly, everything seems fine when I grompp,
>but when I insert it as a co-solvent, it shows like that I never did claim any bond angles, dihedrals, .... even when I #include its .itp and change #mols in my new topology.
You need to work out what is different in the two cases. The diff
    tool can be useful here. There is no fundamental difference in the
    .top construction for the two cases you are considering - only in
    construction of the initial coordinates.

>I guess the problem is if I do not claim the co-solvent as a protein, ff will not go to ffbonded.itp to recognize the new interactions.
>Is there any other file for co-solvent interactions I need to change?
The ffbonded.itp file is #included regardless of what you name your
    moleculetypes. You may not be #including the correct one - but then
    again I think you should only have the standard one in the first


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