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

Shulin Zhuang shulin.zhuang at gmail.com
Tue Mar 21 03:45:06 CET 2006


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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