[gmx-users] Molecular Dynamics basics...

[Mark Abraham]

On 21/02/2012 12:11 AM, prashant kurkute wrote:
> Hi GROMACS users,
>                             I am a very novice to GROMACS.. ..
> My question may be very simple but very important to me..!!!
> These may be very basics...
>
> 1.  What is the meaning of comm_mode and nstcomm..
>      I read the manual but unable to digest it..so please
>      explain in more detail along with its effect on system..

http://en.wikipedia.org/wiki/Flying_ice_cube

>
> 2.  When I am want to study self assembly of protein what
>     should my comm_mode -linear or angular or none ??

You choose based on the above.

>
> 3. what is the meaning of emtol in minimisation proces??
>     Should I take emtol value more or less to come to minimum energy
>     state ??? 

What's not clear in manual section 7.3.5?

> the structure on which I am working is not having any
>      crystal or NMR structure , so I need the maximum energy
>      minimised structure
>
> 4.  When I am doing energy minimisation the gromacs shows
>     (potential energy= -2.07)
>     conjugate gradient step wise to small or no change in energy .
>     converged to machine precision in 15881 step
>     but dindn´t reach to the requested Fmax<10

You are minimizing a noisy function (cutoffs), so oscillation or 
apparent stagnation near a stationary point can occur. See manual 3.10

>    What should to do??
>    or the structure I get is energy minimised or not..???

That depends what you want to do with it next. For MD, it's probably fine.

Mark