[gmx-users] doubts on gen-pairs

[Dommert Florian]

On Mon, 2012-05-14 at 11:55 +0200, Bala subramanian wrote:
> Dear gmx-users, I have some doubts on the manual pages. Kindly help to
> understand the same.
> 
> 
> Section 5.7.1 Page 129
> 
> 1) gen-pairs: Setting ‘yes’ generates 1-4 parameters that are not
> present in the pair list from normal Lennard-Jones parameters using
> fudgeLJ.  
> 
> 
> Is there any way that I can see/write the generated parameters in a
> file.
> 

Hi Bala,

yes with gmxdump, you can extract all necessary topology information
from the tpr file.

> Section 5.7.1 Page 130
> 
> 2) Note that gen-pairs, fudgeLJ, fudgeQQ, and N are optional. fudgeLJ
> is only used when generate pairs is set to ‘yes’, and fudgeQQ is
> always used.
> 
> Does it mean that if i specify gen-pairs as "no" and give the pair
> parameters explicitly in the topology file, scaling of LJ would be
> ignored. I simply want to check the consistency in the energies using
> gen-pair:yes and gen-pair:no (giving the parameters explicitly). 
> 
> 3) Section 5.7.1 Page 130
> 
> [ dihedrals ] : …. If you want to include Ryckaert-Bellemans type
> dihedrals in a topology, do the following (in case of e.g. decane):
> 
> [ dihedrals ]
> 
> ; ai aj ak al funct c0 c1 c2
> 
> 1 2 3 4 3
> 
> 2 3 4 5 3
> 
> and do not forget to erase the 1-4 interaction in [ pairs ]!
> 
> Someone please help me to understand why the 1-4 interaction should be
> omitted for RB type dihedrals ?.
> 

This is also a point I did not understand, when building the itp files
for my ionic liquids. I explicitly checked the influence and realized,
that for RB dihedrals the corresponding 1-4 interactions are only
calculated, if the respective atoms are listed in the pairs section. No
matter how nexcl or gen-pairs is set. 


Cheers,

Flo




> Thanks,
> Bala
> 
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-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
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