[gmx-users] Re: please guide me

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Nov 15 12:33:59 CET 2006


Well, I'll answer anyway...

>  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..

I do mind if people start asking me to do their homework. Since you're
totally new, run the tutorials provided with Gromacs and on
http://nmr.chem.uu.nl/~tsjerk/MDCourse/ (which is the same as the one
hosted by the Groningen group, but then online :p). Read about doing
MD, for instance the book Molecular Modelling from Andrew Leach. And
be sure to be acquainted with both the theory and the practice of MD
on a standard system (e.g. lysozyme) before taking another step.

> sir
>  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
> track.

Didn't I reply to one of your mails mentioning the steps you should
take in setting up a simulation? If not, check the recent archives for
mails concerning setting up and running simulations (basic),
especially one I replied to. It didn't go like this:

>  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.

Now spend a brief moment thinking what would happen if you have a
molecule in vacuum and you say you want to simulate it at constant
pressure (i.e. turn the 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.

Energy minimization is not about RMSD.., did you consider checking the
energy? Think of the reasons to perform energy minimization and, as an
excercise, think of the energy terms you should be particularly
interested in.

>  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?

Don't. Don't even think of going there, without understanding
molecular simulations of 'ordinary' biological systems, both in terms
of theory and practice. Besides that, simulations of non-standard
systems require even more knowledge, for instance regarding the
determination of parameters.


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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