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
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