[gmx-users] Fwd: please guide me

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Nov 15 10:37:48 CET 2006

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---------- Forwarded message ----------
From: nur avneet <nuravneet at yahoo.co.in>
Date: Nov 15, 2006 6:25 AM
Subject: please guide me
To: tsjerkw at gmail.com

 I have a sequenec that i need to optimise first in vaccum then in
solvent..as i am new to gromacs please guide me if i am on the right

 1. First i give the sequence an in vaccuo steepest descent run
(emtol=1000 in mdp file)
 2. then i give the sequence an in vaccuo conjugate gradient run
(emtol = 100, then 50, 10, 5 and 2 in the mdp file)
 3. next i give it an md step in vaccum with temp & pressure coupling on.
 4. I view the trajectory and if i find the rmsd quite less then i
proceed to adiing the box, else i repeat the md in vaccuo step by
increasing the time.
 5. Now i add the box and then water. Next i give it a position
Restraint run and then the md run.

 Is this the right method?
 Also, as my sequence contains peptoid residues (sidechains are
appended to the amide nitrogen rather then alpha carbon) i am unable
to calculate the dihedral angles. How to proceed?
 How can i set the dielectric constant of my choice?

 this is a totally new field to me and i have very little guidance
from my lab...all is what i am doing..So please dont mind if i am
disturbing you..

 Thanks for your help and valuable guidance.

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Tsjerk A. Wassenaar, Ph.D.
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623

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