[gmx-users] hi

[Tsjerk Wassenaar]

Hi Santosh,

For one thing, you don't want to use the gmx force field. For the rest, you
can safely listen to Lars ;) But it is in general good to read a bit on the
background of the force fields and to read papers regarding the types of
systems you are trying to simulate. From these you can aso get a good idea
about the other parameters to use.

Cheers,

Tsjerk

On 3/25/06, Lars Schaefer <Lars.Schaefer at mpi-bpc.mpg.de> wrote:
>
> hi santosh,
> which force field to use usually dependes on your system. E.g., for DNA,
> the AMBER force field is often used. For proteins, you might want to use
> GROMOS96 or OPLS, which are quite popular these days. However, this does
> not necessarily mean that the other force fields, such as GROMACS
> (ffgmx) are worse for your particular system.
> In principle, some force fields are all-atom (e.g., OPLS-AA) and some
> have united atoms for aliphatic CHn groups, e.g. ffgmx.
> Lars
>
>
> santosh naik wrote:
>
> > hi friends
> >
> > i m santosh naik.friends i m new to this field so i m facing a lot of
> > problems dealing with this program.so i wants to start up with
> > simple simulations like proteins in water. my problem is which force
> > field i should use in *pdb2gmx* is it default one or some other please
> > can any one will help me to solve my problem?
> >
> > thanking you
> > santosh naik
> >
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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