[gmx-developers] Total dipole incorrect in energy file

[David van der Spoel]

On 1/25/10 10:12 PM, Tsjerk Wassenaar wrote:
> Hi,
>
> Isn't it possible to update the dipole from displacements?
>
>    
I don't think so because at each time step you can have many 
displacements of atoms over PBC borders.
> 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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>>      
>
>
>    


-- 
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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