[gmx-users] Molecular Dynamics basics...
tinucukki at gmail.com
Mon Feb 20 14:11:05 CET 2012
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..
2. When I am want to study self assembly of protein what
should my comm_mode -linear or angular or none ??
3. what is the meaning of emtol in minimisation proces??
Should I take emtol value more or less to come to minimum energy
state ??? the structure on which I am working is not having any
crystal or NMR structure , so I need the maximum energy
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
What should to do??
or the structure I get is energy minimised or not..???
please give me your valuable advice..These help me a lot
Thank you in advace !!!
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