[gmx-developers] Question about MM point charges in QM/MM calculation

[Pia Toelle]

Thanks for the comment and your interest.


I still would like to get informations about the MM-atom list
(mm->xMM[i][..],mm->MMcharges[i]) and how I could change it, so that all
MM atoms are included not considering the cut-off, because we would like
to print out all (!) MM atoms (and their charges).
Please tell me if a change of the (t_MMrec)-variable mm could cause
problems for the MM-part of the routine or is  the (t_MMrec)-variable mm
only used in the QM part.
Or would it be possible to print out all MM atoms + charges at an other
point in the program? Where?

Thanks in advance.

Pia Toelle

BCCMS
Uni Bremen
Am Fallturm 1
28359 Bremen
Germany



Gerrit Groenhof wrote:
> Hi,
> 
> We did a gmx-dftb interface that used function calls from the linked
> dftb librarysome time ago. That was in 3.3.3, but I never found the time
> to pt it in 4. ALso I remember some compilation issues with the dftb
> code on 64 bit machines. I can send you the code if you're interested.
> 
> For QM/MM the MM atoms are indeed set with the cut-off options. Although
> for dftb it is not very difficult, I have never found the time or need
> to complete the ewald implementation.  To avoid duplications, I suggest
> we finish the PME implementation for the DFTB code together. Contacting
> me off-list  is probably more convenient if you are interested.
> 
> BEst,
> 
> Gerrit
> 
> 
> 
> 
> On 30 Jan 2009, at 18:09, Pia Toelle wrote:
> 
>> Hello.
>>
>> I have got some questions concerning the MM-atom-list in a QM/MM
>> calculation.
>>
>> We do QM-MM calculations using the Gaussian interface (gromacs-3.3.3),
>> but modified the code to be able to use DFTB instead of Gaussian
>> (www.dftb.org).
>> Our (MM-)system is a SiO2-surface (with periodic boundary condition;
>> full).
>> We use PME and DO NOT (!) define proper charge groups for the surface
>> structure, every atom forms its own charge group. Number of MM atoms
>> ~1900.
>> (The proper definition of charge groups in our system is not obvious or
>> even impossible, as it is a solid and a periodic system)
>>
>> We noticed, that the MM system considered in the QM calculation does not
>> consist of the entire MM system. The point charges
>> (mm->xMM[i][..],mm->MMcharges[i]) that are written to input.com (by
>> qm_gaussian.c) are only those of the MM atoms in the vicinity of the QM
>> atoms. The list of MM atoms in the vicinity of the QM-zone is set (as
>> far as we can see) using the neighbor-search algorithm depending also on
>> the charge groups (in ns5_core.c). Please correct me if I am wrong at
>> some point.
>> Is it right, that the cut-off for the QM/MM - neighbor search is set by
>> 'rcoulomb' in the mdp-file? Or 'rlist'?
>>
>> Anyhow, we would like to print out all (!) MM atoms (and their charges).
>> How to solve this problem?
>> Is there a simple way to put all MM atoms in the mm list? And please
>> tell me if a change of the (t_MMrec)-variable mm could cause problems
>> for the MM-part of the routine or is  the (t_MMrec)-variable mm only
>> used in the QM part.
>> Or would it be possible to print out all MM atoms + charges at an other
>> point in the program? Where?
>> I am grateful for any helpful information or idea.
>>
>>
>> Thanks in advance.
>>
>> Pia Toelle
>>
>> BCCMS
>> Uni Bremen
>> Am Fallturm 1
>> 28359 Bremen
>> Germany
>>
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> 
> -- 
> Gerrit Groenhof
> MPI biophysical chemistry
> Goettingen
> Germany
> http://wwwuser.gwdg.de/~ggroenh/
> 
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