[gmx-developers] Total dipole incorrect in energy file

[David van der Spoel]

On 1/25/10 5:35 PM, Berk Hess wrote:
> Hi,
>
> We can't make molecules whole in the general case with DD.
> But also the dipole moment will only make sense for systems without
> molecules with net charge.
> So I think we should remove it from the energy file.
>    
OK, shall I do that in the master branch?

> This will mean that we can not append to old energy files, you will get
> a fatal error in that case.
>    
That is already implemented I presume?

> Berk
>
> David van der Spoel wrote:
>    
>> Hi,
>>
>> it used to be so that mdrun did not break molecules. However, nowadays
>> it does, even though they are fixed before writing the coordinates. I
>> suspect however that the broken molecules are not fixed before
>> computing the total dipole, which is stored in the energy file. The
>> total dipole is used for computing the dielectric constant in g_dipoles.
>>
>> With the current g_dipoles I get good dielectric constants when using
>> the coordinates, and insane (500) when using the energy file.
>>
>> If this observation is correct we can do two things:
>> - fix the coordinates at every step before computing the total dipole
>> - not compute abd save the total dipole at all and remove the -en
>> option from g_dipoles
>>
>> I guess the decision depends on whether the CPU time for reconstrucing
>> the molecules before computing the total dipole is large or not. Maybe
>> Berk can comment on that, obviously there is a reason for not doing it
>> every step.
>>
>>      
>    


-- 
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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