Hi Santosh,<br>
<br>
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. <br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 3/25/06, <b class="gmail_sendername">Lars Schaefer</b> <<a href="mailto:Lars.Schaefer@mpi-bpc.mpg.de">Lars.Schaefer@mpi-bpc.mpg.de</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
hi santosh,<br>which force field to use usually dependes on your system. E.g., for DNA,<br>the AMBER force field is often used. For proteins, you might want to use<br>GROMOS96 or OPLS, which are quite popular these days. However, this does
<br>not necessarily mean that the other force fields, such as GROMACS<br>(ffgmx) are worse for your particular system.<br>In principle, some force fields are all-atom (e.g., OPLS-AA) and some<br>have united atoms for aliphatic CHn groups,
e.g. ffgmx.<br>Lars<br><br><br>santosh naik wrote:<br><br>> hi friends<br>><br>> i m santosh naik.friends i m new to this field so i m facing a lot of<br>> problems dealing with this program.so i wants to start up with
<br>> simple simulations like proteins in water. my problem is which force<br>> field i should use in *pdb2gmx* is it default one or some other please<br>> can any one will help me to solve my problem?<br>><br>
> thanking you<br>> santosh naik<br>><br>>------------------------------------------------------------------------<br>><br>>_______________________________________________<br>>gmx-users mailing list
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Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>