[gmx-users] Clarification!

[Swetha Vijayakrishan]

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.

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?

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?

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