[gmx-users] Assignment of new velocities for multi-runs

[James Starlight]

Peter, Justin,

Thanks alot for the comments.

In the current work I do short simulation of the membrane receptors (
100 ns) started from different conformations of that proteins in the
common physical conditions and than do Essential Dynamics analysis of
the calculated trajectories and compare eigenvectors from both of
them. It's intresting to me might the different starting velosities
influence on the overal dynamics of the protein- i.e sampling of
different sub-states ( which would reflect on the eigenvectors from
that runs)

Thanks again

James

2012/9/29 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 9/29/12 3:08 AM, Peter C. Lai wrote:
>>
>> If the system is already well equilibrated previously then you can
>> probably
>> safely reassign velocities during NPT. The best way to do this would
>> probably
>> be to take the equilibrated checkpoint file as the starting point:
>>
>> grompp -f genvel-yes-npt.mdp -t previous.cpt ...
>>
>> You'll still have to wait some ns for the system to reequilibrate so data
>> comparisons between the runs for the first several ns will not be
>> meaningful,
>> so ultimately, the question is what you do you hope to gain from
>> reassigning
>> velocities at the beginning?
>>
>
> I disagree with the approach of reassigning velocities at the outset of NPT.
> Doing so can lead to instabilities in the pressure coupling algorithm and
> the system may crash.  The simplest answer is to just use different starting
> velocities at the very beginning of the workflow (i.e. velocity generation
> at NVT with different values of gen_seed).
>
> -Justin
>
>
>> On 2012-09-28 11:59:02PM -0700, James Starlight wrote:
>>>
>>> Dear All!
>>>
>>> I'd like to perform several simulations of the membrane protein
>>> started from the common conditions which differs only in the initial
>>> velocities ( for each simulation random speed distribution will be
>>> used from the Maxwell distribution).
>>>
>>> Because I simulate membrane protein the long equilibration phase is
>>> required for that system. I've noticed that new velocities sets are
>>> assigned in the NVT phase of equilibration (100ps) after which more
>>> prolongest npt equilibration (10ns) is followed.
>>>
>>> Does it require that new velocities always be assigned exactly during
>>> equilibration of my system ? Could I use new velocities in the
>>> production md run instead ? In the latter case my system will be
>>> equilibrated with one velocities but further production MD will be
>>> with another velocities each time? (so in latter case I can avoid long
>>> equilibration phase for each simulation).
>>>
>>>
>>> James
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>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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