VMD-L Mailing List

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Sat Mar 28 2009 - 18:59:33 CDT

Dear All,

for NAMDEnergy in VMD, how do I change the namd-run-command?

I guess I need to change the parameters:
runext
runextcommand

I tried:
namdenergy -dihe -sel [atomselect top protein] -runext 1 -runextcommand
"/usr/bin/mpirun -np 5 /softlib/exe/ia64/bin/namd2"

but that still doesn't work.

Thank you,
Best,
Sebastian

Axel Kohlmeyer wrote:
> On Thu, 2009-03-26 at 03:30 -0400, Francesco Pietra wrote:
>
>> Hi:
>>
>
> francesco,
>
> you can "overlay" multiple representations with different selections
> in VMD. no scripting required. please see the various visualization
> tutorials on the TCBG homepage and the VMD user's guide for examples.
>
>
>> To the patience of those who now, some simple howto questions about a
>> a protein carrying a docked small molecule or peptide. Everything in
>> the same pdb file.
>>
>> How to select the docked molecule per residue(s) name and "stain it",
>> i.e. highlight it by, say, tube bonds and color by element, while the
>> receptor protein is shown in ribbon (clearly, now, when I set "ribbon"
>> the small, non peptidic molecule disappears).
>>
>> How to grasp which is which on the fly, i.e., for example, revealing
>> the residue names and numbers by simply pointing the cursor to them,
>> or what else is appropriate to do with vmd.
>>
>
> you can label or inquire about stuff using the options from the
> "Mouse" menu. some of the output will be to the console, though.
> anything more sophisticated has to be scripted, but it is worth
> investing the time to learn how to do this, as then few things are
> impossible to do.
>
>
>> How to map residues of the receptor around residue(s), or atoms, of
>> the docked molecule?
>>
>> All that in the perspective that the said complex is added of a
>> vmd_plot representation, and I want also to know which is which with
>> respect to that plot.
>>
>
> there is _no_ 'vmd_plot' representation. you are referring to the
> output from a script that just generate a large number of graphics
> objects. those are placed in the same coordinate system as your
> molecule, but otherwise independent from it.
>
>
>> Is it any way to build a file for molecular dynamics directly from
>> those representations?
>>
>
> yes. there is already the autopsf tool that can be used as a frontend to
> build topologies with psfgen. the next release of VMD will also contain
> a topology tools package, that allows to manipulate or create topology
> files independent from psfgen. i've written a front and back end for
> LAMMPS and HOOMD with it and plan to do others as well. gromacs has been
> requested already.
>
>
>> Unfortunately, I am unfamiliar with tlc, coming from python. But now
>> it seems that I can only progress in this study with vmd.
>>
>
> if you don't know it, you have to learn it. as painful as it may seem,
> this is an investment that will pay off.
>
> cheers,
> axel
>
>
>> thanks for your understanding
>>
>> francesco pietra
>>
>
>