[gmx-users] modifying source code

[Mark Abraham]

On 15/04/2010 12:32 PM, Sang-Won Park wrote:
> Hello all,
>
> I am trying to modify the source code.
> My simulation system consists of several huge modecules disolved in a
> liquid. The relative orientation among the huge molecules is not
> significant in the system, and I concern structural properties only, not
> dynamic properties, in the equilibrium state. I guess it'll take very
> long time to equilibrate this because it's a huge system.
>
> So here's an idea. I sum all the forces exerted on a huge molecule and
> move the center of mass of it translationally only without rotation, so
> I can save the computation time.

I don't see why this would give you a valid ensemble, or save 
computation time. You still need to evaluate every force and move every 
atom - you're just adding in an intermediate step that would slow things 
down a lot.

> To do this, I have to change the source code. So, I read mdrun.c and
> several source code files, but I could hardly understand them.
> When I used dlpoly, the reference manual helped me a lot understand the
> source code. It has explanations on all the variables and subroutines,
> but I can't find one for gromacs.
>
> I guess it's hard to answer my question and to make me understand the
> source code through email. If there exists such a manual on the source,
> please let me know how to get it.
> Thank you in advance.

There's a mixture of stuff available here 
http://www.gromacs.org/Developer_Zone/Programming_Guide but it may or 
may not suit your purposes.

Mark