[gmx-developers] Fluctuation properties

[hess at sbc.su.se]

> On 1/27/10 9:11 PM, Michael Shirts wrote:
>> Hi, David-
>>
>>
>>> we are trying to get accurate fluctuation properties out of mdrun. For
>>> this purpose I have built in a calculation of the enthalpy (Etot + pV)
>>> and store that in the energy file for maximum accuracy.
>>>
>>> Which NPT algorithm/integrator combination is recommended that
>>> minimally
>>> disturbs the fluctuations?
>>> Initial tries with Leap Frog/Nose Hoover/Parrinello Rahman give us
>>> fluctuations that are quite a bit too large (using GAFF):
>>> methanol: cp_exp=81, cp_gaff=141
>>> ethanol:cp_exp=122, cp_gaff=211
>>>
>> Sounds like a great time to try the velocity verlet code with the
>> Martyna-Tuckerman-Tobias-Klein pressure integrator that I just
>> integrated into the CVS last month!   Theoretically, it should give
>> the correct fluctuations.
>>
>> It conserves the conserved quantity correctly -- but there might be
>> something else subtle going on, so this would be a good test to run.
>>
>> To use:
>> use 'md-vv' for integrator
>> and 'MTTK' for pcoupl.
>> tcoupl should remain 'Nose-Hoover'.
>>
>> (Yes, I need to catch up the documentation -- I've been working on it,
>> but it isn't checked in yet).
>>
>
> Trying to run as you advertise it (512 TIP4P/PME/LJ-Cut):
> Statistics over 7101 steps [ 5.0000 thru 19.2000 ps ], 2 data sets
> All averages are over 7101 frames
>
> Energy                      Average       RMSD     Fluct.  Tot-Drift
> -------------------------------------------------------------------------------
> Total Energy               -17316.8    169.118    154.362   -239.337
> (kJ/mol)
> Conserved En.              -17304.4    7.48269    1.90526    25.0665
> (kJ/mol)
>
> Is this as expected?
>

I would use shift with buffer for LJ.

Berk

> And another point: is this supposed to run in parallel? It runs fine on
> 1 cpu but gives me a SEGV on 4 cores...
>
>> Note also that 'md-vv-avek' is another integrator that uses the
>> average of the half step kinetic energies to determine the
>> temperature, instead of the full step velocities.  I'm not 100%
>> certain about the validity of this way of doing things this way when
>> combined with full step pressure control, so run 'md-vv' also if you
>> do 'md-vv-avek', just for comparison's sake.
>>
>> Note that pV should be the volume times the applied pressure, not the
>> instantaneous pressure -- this was wrong a few months ago,but I posted
>> a correction 2-3 months ago.  Don't know what version you are using
>> for these calculations, so that may not be an issue anyway.
>>
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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