Justin A. Lemkul
jalemkul at vt.edu
Fri Dec 4 16:59:05 CET 2009
pawan raghav wrote:
> 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?
Visit the Grace website and follow whatever download and installation
instructions they provide.
> 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)?
I don't fully understand this question. The longest cutoff must be shorter than
half the shortest box vector to satisfy the minimum image convention. This is
usually accomplished by setting a reasonable value of -d when using editconf,
checking the box vectors that result and setting cutoffs appropriate for the
force field of interest.
> 3. In fullmd_sol.mdp file how to find the time step value because I
> don't have confirmation about that.
You specify time step with the dt parameter.
> 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
Good suggestion. There's lots of literature on the topic.
> (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.
For (b) and (c), it sounds like you need to do some tutorials and background
reading. Might I suggest:
> 5. How to save screen of cygwin (general question)
Copy and paste from the command line? There's a screenshot mechanism somewhere
in Windows otherwise.
> Please solve these problems if you can I am thankful to you.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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