[gmx-users] Re: How to generate itp files of small moleclues for gromos96 force field

[Shulin Zhuang]

By the way, for the optimal  setup of molecluar dynamics, there are some
difference for gromacs and gromos,  such as in the mdp file, GROMOS 96 force
field uses nstlist = 5 and rvdw = 1.4.
Can anyone give me a standard mdp file to do MD simulation with gromacs
package using gromos96 force field?

Great thanks


On 3/21/06, Shulin Zhuang <shulin.zhuang at gmail.com> wrote:
>
>  Dear All,
>
> I use gromacs version 3.3 to perform a simulation on a protein-drug
> complex. I chose the gromos96 53a6 force field. But how to generate the
> parameter file of the drug fo gromos96 53a6 force field. The Dundee PRODRG
> server produce files in format of gromacs/gromos87.
> But the produce files of drugs such as itp file is not full agreement with
> gromos96 format. For example,  in the itp file of the drug,  as far as the
> bonds are  concered, in gromacs, the funct is set to 1,while in gromos96 ,it
> is 2.  Should I just change the funct value to 2  to keep it in agreement
> with gromos96 force field? For the atom type, I can edit them. But the bonds
> parameter is difficult for me to convert them to gromos96 force field. Would
> anyone give me any suggestion?
>
> best regards
>
> --
>    Shulin Zhuang
> Chemistry Department
> Zhejiang University PRC
> shulin.zhuang at gmail.com
>



--
   Shulin Zhuang
Chemistry Department
Zhejiang University PRC
shulin.zhuang at gmail.com
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