[gmx-users] a residue move in extremely large scale in MD

Acoot Brett acootbrett at yahoo.com
Sun Aug 12 01:25:01 CEST 2012

Dear Albert,

I hope I can support my MD results with some bioinformatics data. For example, it indicates the highly movavle residue I mentioned in my previous e-mail is not conserved at all, and it is only specific that structure.

For your 10X with different seed simulation, does it mean the production time scale changes to 100 ns, or does it mean I run 10 rounds of 10 ns MD to vierify the results? For GROMACS, the seed is choosen automatically, do we have the method to choose it manually?

For the converge you mentioned, I agree for some simulations 10 ns is not enough, but I think within 10 ns if what you want to determine has converged, that would be fine. For converge, which parameters do you use to decide whether it has converged?
There are some Journals accept computational biology research results without the support of biochemistry data, can you suggest these Journals to me?

I am looking forward to getting your reply.



----- Original Message -----
From: Albert <mailmd2011 at gmail.com>
To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, 11 August 2012 3:57 PM
Subject: Re: [gmx-users] a residue move in extremely large scale in MD

you have to submit 10X with different seed simulation to confirm your results. 10ns is not converged for some simulation, you should also extend it in nowadays timescale level.
Moreover, if you don't have biochemistry data to support your idea, nobody will believe your results.

good luck

On 08/08/2012 08:55 AM, Acoot Brett wrote:
> Dear Catch ya,
>   I have watched the trajectory of the simulation. Besdies, I got the PDb file for the whole 10 ns MD every 500 ps. Then I compared all the PDB files generated, and it confirms that 1 specific residues moves in an extremely large space.
>   Can you give me an explaination on it?
>   Cheers,
>   Acoot   

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