[gmx-developers] Which integrator/coupling for accurate fluctuations?

[David van der Spoel]

On 1/27/10 8:56 PM, hess at sbc.su.se wrote:
> Hi,
>
> But you don't really know how accurate the force-field is, do you?
>    

Of course, but this is what we want to establish. But then we have to 
eliminate other sources of error. We will try your suggestions, thanks.

> You should be checking the conserved energy quantity to see
> if that is well conserved and does not fluctuate too much.
> I think this is not calculated for LF NPT.
> I think what you want is Michael Shirts' newly implemented
> VV integrator with proper coupling, which I think is Nose-Hoover + MTTK.
> This should give the best possible integration.
> You should then also get the conserved quantity, so you can actually
> check your integration.
>
> Berk
>
>    
>> Hi,
>>
>> 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
>>
>> This is from equilibrated boxes with 512 molecules. Any hints,
>> suggestions?
>>
>> --
>> 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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>>      
>    


-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++