On 30/03/2010 12:20 AM, lloyd riggs wrote:
Dear Folks,
I am new to posting here. In any case, I wanted to set initial trajectories
for two large macromolecules.
Why? The usual reason for molecular dynamics is to observe the *dynamics*.
Basically I am using gromacs for several things, on would be simple energy
calculations.
They won't tell you much. Free energies of interaction sound like what
you might want.
For this I wanted to take to proteins, or protein and larger ligands and set an
initial trajactory for these in the solvent so that they collide in a specific
way based on Docking, other things etc...as a quick and dirty type run.
There won't be a quick way, because it's not something that is feasible
with explicit-solvent biomolecular MD. The amount of sampling required
even to use the pull code with a preconceived protein-ligand orientation
is likely to be prohibitive. If you permit the ligand its freedom, the
cost of enough sampling to solve the problem explodes dramatically.
You really sound like you want to use a docking program.
Does anyone have a really simple protocol,
such as a) input output
b) input output, etc...
I have read several things in the manual that state this is possible, but I
wanted to avoid a day of trying to get it to work, and just get it to work
quickly.
We'd all like things to be quick, but doing novel investigations never
is. People new to the field should avoid such investigations while they
acquire experience. :-)
Mark
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