VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Mar 28 2009 - 19:36:45 CDT

Hi Sebastian,
try making your new command the argument to runext, i.e.,
-runext "/usr/bin/mpirun -np 5 /softlib/exe/ia64/bin/namd2"

It would be helpful to post the error message that you get as well...

Best,
Peter

Sebastian Stolzenberg wrote:
> 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
>>>
>>
>>