[gmx-users] Replicating an experiment

[NG HUI WEN]

Thanks Mark, message noted:)

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Sunday, December 26, 2010 6:03 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Replicating an experiment

On 26/12/2010 4:37 AM, 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

Do be aware that density will change if you do NPT at different T, and 
you'll need to re-equilibrate regardless.

Mark

> 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.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se
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