[gmx-users] RE:directed trajectories

Mark Abraham Mark.Abraham at anu.edu.au
Mon Mar 29 17:19:13 CEST 2010

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. :-)


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