[gmx-users] how to repeat simulation correctly?
Felipe Pineda, PhD
luis.pinedadecastro at lnu.se
Wed Nov 21 13:03:47 CET 2012
So how would you repeat the (let be it converged) simulation from
different starting conditions in order to add that valuable statistics
I think this was Albert's question
On 11/21/2012 12:41 PM, Mark Abraham wrote:
> If a simulation ensemble doesn't converge reliably over a given time scale,
> then it's not converged over that time scale. Repeating it from different
> starting conditions still adds valuable statistics, but can't be a
> replicate. Independent replicated observations of the same phenomenon allow
> you to assess how likely it is that your set of observations reflect the
> underlying phenomenon. The problem in sampling-dependent MD is usually in
> making an observation (equating a converged simulation with an observation).
> On Wed, Nov 21, 2012 at 8:12 AM, Albert <mailmd2011 at gmail.com> wrote:
>> I am quite confused on how to repeat our MD in Gromacs. If we started
>> from the same equilibrated .gro file with "gen_vel = no" in md.mdp,
>> we may get "exactly" the same results which cannot be treated as reasonable
>> repeated running. However, if we use "gen_vel=yes" for each round of
>> running, sometimes our simulation may not converged at our simulated time
>> scale and we may get two results with large differences.
>> So I am just wondering how to perform repeated MD in Gromacs in a
>> correct way so that our results can be acceptably repeated?
>> thank you very much.
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| Luis Felipe Pineda De Castro, PhD |
| Computational Chemist - Postdoc |
| Computational Chemistry and |
| Biochemistry Laboratory |
| School of Natural Sciences |
| Linnaeus University |
| SE-391 82 Kalmar |
| Norrgård, room 311 |
| Sweden - Sverige |
| Phone: ++46-480-44 6329 |
| Mobile: ++46-76-8420572 |
| E-Mail: luis.pinedadecastro at lnu.se|
| Web: lnu.se |
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