# [gmx-users] Question about topologies

Erik Marklund erikm at xray.bmc.uu.se
Fri Jun 18 12:12:00 CEST 2010

```Thanasis Koukoulas skrev:
> Hello
>
> [ atomtypes ]
> ; type mass charge ptype c6 c12
> CH3 15.035 0.000 A 9.0638e-3 2.5206e-5
> CH2 14.027 0.000 A 5.8108e-3 2.2071e-5
> CS2 14.027 0.000 A 5.8108e-3 2.2071e-5
> OS 15.999 0.000 A 8.8147e-4 4.2477e-7
> OA 15.999 0.000 A 2.3465e-3 1.7802e-6
> HO 1.008 0.000 A 0.0000e00 0.0000e00
>
> at atomtypes i can give c6 and c12 values and gromacs will generate
> the c6ij and c12ij values from the formulas i have chosen with
> selecting combination rule Am i right????
>
> in my case i gave c6 and c12 as c6i=4*ei*σi^6 and c12i=4*ei*σi^12 and
> i chose combination rule 1. so gromacs will generate the c6ij and
> c12ij as c6ij=sqrt(C6iC6j) and c12ij=sqrt(c6i*c12j)
>
> So if in my topology I put [nonbond_params] what happens then? the
> values from [nonbond_params] c6 and c12 are being replaced by the
> values gromacs finds from the equations???
>
> for example
>
> if i have
>
> [nonbond_params]
>
> CH3 CH3 5e-3 6e-5
>
> and gromacs calculates from the [atomtypes] are different lets say (i
> didnt do the calculation it is an assumption value) 3e-2 and 3e-5
> which values gromacs accepts?
> i have read the manual but it isnd clear how this works.
>
> please someone enlighten me.
>
> thanks
>
>
HI,

One good way of finding out is to generate two tpr-files and compare
them with the help of gmxdump.

--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

```