Priya Chandran wrote:
Hello,
I am a beginner in GROMACS and I am using GROMACS to analyse the
solution structure of protein in water after initial homology/abinitio
modelling. I have already run a search on the gmx_users list for my
queries. There are a few basic questions i would like to ask.
Welcome.
1. In the md integrator, what is the total simulation time used in
simulation of peptides in general? I'm currently using 200ps, consisting
of nsteps=100000, and dt=0.002 and the rmsd graph has not reached a
plateau region still.
This is totally dependent on the system in question and what you expect
the time-scale of relevant motions to be. I'd expect 200ps is at least
an order of magnitude too short to have any basis for confidence that a
solution structure is stable for a given forcefield.
2. Is minimisation in GROMACS only used as a precursor to the
md-simulation to remove bad contacts, or can we also use it effectively
to minimize a raw modelled ab-initio structure.?
Well, yes, you can use it for this - they're both the same objective,
really.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
