[gmx-developers] Accessing forcefield data

[Martin Ulmschneider]

Thanks!! Got it all running... just one last paranoid question, will 
adding a force in Gromacs cause any problems with pressure or 
temperature coupling? I added it just above calc_f_el, which i assume is 
another extra force. Is there anything i should keep in mind?

My system is a normal protein which feels the effect of the forcefield 
and my extra force.

Best wishes,
Martin


David wrote:
> On Thu, 2004-07-08 at 18:02, Martin Ulmschneider wrote:
> 
>>Thanks, i worked it out. Now i would like to access the c6 and c12 
>>values from the Lenard Jones (vdW) interaction. Could you point me to 
>>the right routine? I've looked at mk_nbfp in force.c, which i think has 
>>the cross terms for all atomtypes, but how can i find the values for 
>>some atom j?
> 
> You index the matrix with the atom type in mdatoms->type
> 
>>Many thanks in advance!
>>Best wishes,
>>Martin
>>
>>David wrote:
>>
>>>On Tue, 2004-07-06 at 23:17, Martin Ulmschneider wrote:
>>>
>>>
>>>>Hi,
>>>>
>>>>I am adding an extra force in gromacs. This force depends on the 
>>>>forcefield values of r0 and angle0 (i.e. the forcefield bondlength and 
>>>>angle). Hence i would prefer to access r0 and angle0 in the CODE rather 
>>>>than writing a new forcefield file loader. Is this very difficult to access?
>>>
>>>Not very...
>>>There is a Urey-Bradley term in the bonded forces which should have all
>>>the information you need. (src/gmxlib/bondfree.c)
>>>
>>>
>>>
>>>>Best wishes,
>>>>Martin
>>>>
>>>>David wrote:
>>>>
>>>>
>>>>>On Tue, 2004-07-06 at 21:41, Martin Ulmschneider wrote:
>>>>>
>>>>>
>>>>>
>>>>>>Hi,
>>>>>>
>>>>>>I would like to check the forcefield data (i'm interested in the 
>>>>>>forcefield bond lengths r0 and angles alpha0) in gromacs. Could you 
>>>>>>please tell me which structure they are in and how i can access them? 
>>>>>>E.g. the mass of atom j can be accessed by  mass = top->atoms.atom[j].m. 
>>>>>>Is there a simlar way to access b0 and alpha0?
>>>>>>
>>>>>
>>>>>wouldn't you rather browse through the text files in share/top ?
>>>>>otherwise you'll have to decipher the idef structure of the topology.
>>>>>
>>>>>
>>>>>
>>>>>>Many thanks!!!
>>>>>>Martin
>>>>>>
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