On 12/25/10 6:37 PM, NG HUI WEN wrote:
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?
Yes that is what I meant. Of course you should check that your protein
is not unfolding, or you membrane going into the wrong phase.
Thanks very much indeed!!
________________________________
From: gmx-users-boun...@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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