While running MD simulation I have number of queries mentioned below:
1. When executing xmgrace command it returns the bash command not found,
then how to install GRACE package on windows?
2. When defining the box dimention then how do I know about the distance of
protein (207 residues) from the box wall should be greater than half of the
Cut-Off (1.4nm)?
3. In fullmd_sol.mdp file how to find the time step value because I don't
have confirmation about that.
4. When using grommp command to generate fullmd.tpr file, it will shows 3
notes
(a.) The Berendsen thermostat does not generate
the correct K.E distribution, and suggesting to use v- rescale thermostat
(b.) Why the system has non-zero total charge :
-2.000001e+00
(c.) [file fullmd_sol.mdp, line unknow]: you are
using a plain coulomb cut-off, which might produce artifacts. You might want
to consider using PME electostatics.
5. How to save screen of cygwin (general question)
Please solve these problems if you can I am thankful to you.
--
Pawan
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