[gmx-users] 1-4 columb interaction

[Alok]

Thanks Chris for your detail reply.....
It really help me a lot.

Regards,
Alok

----- Original Message ----- 
From: <chris.neale at utoronto.ca>
To: <gmx-users at gromacs.org>
Sent: Thursday, September 21, 2006 7:08 PM
Subject: [gmx-users] 1-4 columb interaction


Quoting Alok <alokjain at iitk.ac.in>:

> Thanks Chris for your explanation.and I am sorry to bother you by   
> writing a personal mail.
>
> So its mean if I am using default values for genpair (=no),   
> FudgeLJ(=1.0) and FudgeQQ (=1.0), then I am doing scaling for LJ 14   
> interaction only by using separates set of parameters, but not for   
> 1-4 columb interaction, because I am using FudgeQQ =1.0.And in   
> GROMOS96 and in ffgmx force field there is not separate set of   
> parameters for Columb14 interaction.  am  I correct??

Basically correct. However, there is never a second set of parameters  
for coulombic 1-4 interactions--it simply is not possible with  
gromacs-3.3.1, this is the central point that lead to the need for  
Tieleman's 2006 paper that is mentioned below.

> Apart from that in one of your previous mail in gromacs mailing list  
>  .subject : - OPLS and Berger lipid et al Tieleman 2006
> http://www.gromacs.org/pipermail/gmx-users/2006-August/023587.html
>
> you had mentioned
> "However, this 2006 paper appears to be entirely different. If I   
> understand correctly, the main difference is that they "decided to   
> replace the 1-4 interactions in the lipids (both the electrostatic   
> and the Lennard-Jones components) with dihedral potentials.)"   
> because of the inability to scale columbic separately in Gromacs."
>
> So if we use FudgeQQ =0.5 there then what is the problem to direct   
> addition of berger lipid in OPLS force field?? because FudgeQQ is   
> going to apply on all the cases dosen't matter what we are using   
> genpair = yes or no.Why they have to replace the 1-4 interaction   
> with dihedral potential (RB).
>

The problem is that the FudgeQQ for the Berger lipids should be 1.0  
and for OPLS-AA it should be 0.5. There is no way to do this  
analogously to the LJ parameters that can be set in [ pairs ] or [  
pairtypes ].

If you want to base your work on something that has been entirely  
tested and published, then I suggest that you either live with the 0.5  
FudgeQQ scaling for all, or request the new dihedrals from Tieleman's  
lab (although I believe that they are not yet being made available).

If you can accept working with an idea that sounds rigorous but has  
not yet been tested for more than 5ns or published at all, look here  
for the method that I use:
http://www.gromacs.org/pipermail/gmx-users/2006-September/023761.html
and here for Berks much improved suggestion about clean implementaion:
http://www.gromacs.org/pipermail/gmx-users/2006-September/023782.html
(I am sure the set of zeroes in "with additional 0 0 parameters for  
the LJ" read sigma epsilon in some font.)


> eagry waiting for your reply,
> Alok
>
> ----- Original Message -----
> From: <chris.neale at utoronto.ca>
> To: <gmx-users at gromacs.org>
> Sent: Thursday, September 21, 2006 2:05 AM
> Subject: [gmx-users] 1-4 columb interaction
>
>
> You are right that the LJ fudge values don't get applied if
> gen-pairs=no. However, FudgeQQ is always applied. However, one would
> hope that Qiao was correct and the main .itp files at least list the
> correct scaling of LJ 1-4 interactions. Force fields that use
> gen-pairs=no explicitly list 1-4 LJ parameters in the pairtypes
> section. This appears to be the case in the gromos96 force field. For
> example,
>
> [ nonbond_params ]
> ; i    j func          c6           c12
>        OM        O  1  0.0022619536  7.4149321e-07
> [ pairtypes ]
> ; i    j func          c6           c12
>        OM        O  1  0.0022619536  7.4149321e-07
>
> So a 1-4 (pairtypes) and a 1->5 or nonbonded LJ are going to be the same.
>
> The treatment of 1-4 interactions is quite well described in the
> gromacs manual.
>
>
>    ----- Original Message -----
> Thanks Qiao for your reply.
>
> But If I am using genpair = no (GROMOS 96 force field) then there is
> no meaning of  fudgeLJ and fudgeQQ (correct me if I am wrong).
>
> So more specific if I am using GROMOS96 force field then is there any
> scaling for 1-4 columb interaction??
> if yes then how?
>
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