[gmx-users] regarding dimethylated lysine topology file

[Antonia Vyrkou]

Hi, 

the function used by GROMACS is Vd (öijkl ) = kö (1 + cos(nö − ös )), for
proper dihedrals (periodic type).
Take a look at Chapter 4, of GROMACS-4-0 manual.

Antonia



>prasun kumar <prasun30 at gmail.com> said:

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> Respected all
> I drew the structure using the drawing tool available in PRODRG server
> then I went for  topology file generation,but the server is deleting almost
> all the hydrogen atoms while writing the topology file for gromacs
> can any one tell me why it is doing like this?
> 
> another question I got that is
> how to change gromacs topology file to charmm topology file
> (I know for bond length and angle........but for dihedral(improper and
> proper))
> actually i want toi know which function gromacs is using for the calculation
> of dihedrals..........
> thanx in advance
> 
> PRASUN (ASHOKA)
> 
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> Respected all <br>I drew the structure using the drawing tool available in =
> PRODRG server<br>then I went for=A0 topology file generation,but the server=
>  is deleting almost all the hydrogen atoms while writing the topology file =
> for gromacs<br>
> can any one tell me why it is doing like this?<br><br>another question I go=
> t that is<br>how to change gromacs topology file to charmm topology file <b=
> r>(I know for bond length and angle........but for dihedral(improper and pr=
> oper))<br>
> actually i want toi know which function gromacs is using for the calculatio=
> n of dihedrals..........<br>thanx in advance<br><br clear=3D"all">PRASUN (A=
> SHOKA)<br>
> 
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> 



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