[gmx-users] Molecular Dynamics basics...

prashant kurkute 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
     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
   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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