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
thermostat
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:
http://www.gromacs.org/Documentation/Tutorials
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.
-Justin
Please solve these problems if you can I am thankful to you.
--
Pawan
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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