[gmx-users] Fwd: please guide me

[Mark Abraham]

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

That seems reasonable in the abstract. I would do more EM after adding 
water, to relieve bad contacts, then do a position restrained NVT run to 
get the temperature OK, then relax to NPT without position restraints, 
if you want to end in that ensemble.

> 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?

I'm not sure what you mean. If you mean you lack parameters for dihedral 
angles for such peptides, then there is no easy solution. Read the paper 
that describes the development of your force field. Look and see if 
there are any dihedrals defined that are chemically analogous and you 
can borrow them with reasonable confidence. Otherwise, do the 
parameterization work.

> How can i set the dielectric constant of my choice?

See the other thread. You can't do this in an explicit solvation MD 
simulation, which is all that GROMACS does. Implicit solvation MD allows 
you to do this.

> 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..

Knowledge and experience in this and related fields tends to be 
hard-won, and the practitioners are busy people. Many of them value 
reading and answering others questions because of what it teaches (or 
reminds!) them. At the same time, nobody is likely to be able to be a 
personal tutor. I suggest you do all the tutorial material you can find 
on the web (consider those available for other MD packages, like NAMD, 
AMBER, CHARMM and others, or more usefully still for a GROMACS context, 
work out how to do their tutorials using GROMACS; consider subscribing 
to their mailing lists too), get some books on the topic, read the 
existing literature on simulations on systems like yours, and be 
prepared to experiment and work hard. When you have questions, and your 
documentation doesn't answer them, by all means ask a well-posed and 
polite question on a mailing list :-)

Mark