[gmx-users] Replicating an experiment

[NG HUI WEN]

Thank you David for your prompt and useful reply :)  I am in fact simulating a membrane protein.
 
It's good to know I can use the "generate-new-starting-velocity" method. But, do you mind to elaborate a bit more what you mean by "if you simulate long enough"? 
 
I would like to try your suggestion of picking a random structure from an elevated temperature simulation. Can I achieve that by taking my existing membrane protein system, 
1) pass it through grompp with a new mdp (with higher temperature) to produce a new .tpr file 
2) simulate the system for a period (perhaps 1 ns) 
3) take any frame / final structure
4) pass it through grompp again (with original mdp with temperature 300K, gen_seed = -1) to produce the .tpr file for my replicate?
 
Thanks very much indeed!!

________________________________

From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Sat 12/25/2010 10:28 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Replicating an experiment



On 2010-12-25 15.05, NG HUI WEN wrote:
> Dear all,
> Merry Xmas! I have a very quick question here which i'd like to pick
> your brain on, would really appreciate a reply.
> I am planning to replicate an experiment that I have carried out. Just
> wondering what is the best way to do it? I am thinking of changing the
> starting velocity of my system by setting a random number e.g 23412445
> etc in the gen_seed section as below, not sure if it is meaningful to do so?
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = random number
> Thank you for your input!
That will work fine, if you simulate long enough. Consider that the
starting structure may also influence how different your results  will
be, e.g. for a protein in water. For liquids there is no such problem.
You can do a simulation and slightly elevated temperature and pick
structures from that with a different random seed, in order to randomize
your simulations even more.
> HW
> <<
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
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