[gmx-users] Clarification!

[David van der Spoel]

On Wed, 2004-05-12 at 18:34, Swetha Vijayakrishan wrote:
> Hi all,
> 
> I just wanted to clarify 3 things.
> 
> 1. Firstly, can a principal component ananlysis(pca) be done in gromacs.if
> so,how does one go about doing it.
g_covar
g_nmeig

> 
> 2. Secondly, how do i do molecular dynamics of a protein such that only
> the active part of the protein is subjected to the dynamcis and the rest
> of the protein is restrained?
use freeze groups or position restraints

> 
> 3. Is the gromacs forcefield good for simulation of DNA or RNA. if so
> which forcefield do i have to use which would give me the best results if
> i need to simulate a protein in complex with a fragment of DNA or RNA?
> 
no. amber is not yet officially implemented. don't know whether OPLS is
good.

> I would really appreciate if information on the above could be given.
> 
> Regards,
> 
> Swetha
> 
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> 
> --------------------------------------------------------------------------------
> 
> Swetha Vijayakrishnan
> c/o Dr.Shekhar.C.Mande
> Lab of Structural Biology
> Centre for DNA Fingerprinting and Diagnostics (CDFD),
> ECIL Road,Nacharam,
> Hyderabad-500076
> INDIA
> 
> Phone : off # (91)040-27171442
> 
> Email : swetha at cdfd.org.in
>         swethasenorita at yahoo.com
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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