[gmx-developers] Total dipole incorrect in energy file

[Tsjerk Wassenaar]

Hi,

Isn't it possible to update the dipole from displacements?

Cheers,

Tsjerk

On Mon, Jan 25, 2010 at 8:29 PM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist