[gmx-users] xmgrace

[Justin A. Lemkul]

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
> 

-- 
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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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