[gmx-users] the DNA md simulation

Banafsheh Mehrazma bmehrazma at gmail.com
Sat Feb 4 08:27:42 CET 2012

Dear Justin;
I specified the terminal residues in the *.mdp file, just like what in
my force field has (DNA.rtp) mentioned. I wonder if we should some
thing else with it? I mean, when I viewed my molecule with VMD, after
a 5 ns simulation, my terminal residues were not in front of each
other, they are slanted inward the helix.
I don't know, whether it is right or not!

Best regards

On 2/1/12, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Banafsheh Mehrazma wrote:
>> Dear all;
>> Through the MD simulation for a DNA, I wonder whether we should change
>> any options for the terminal bases or not.
> What is it that you think you should change?
> -Justin
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list