[gmx-developers] Re: turn on pdb output after every step.

Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu
Tue Jan 15 09:34:55 CET 2013

On Tue, Jan 15, 2013 at 5:50 AM, santhosh <mesanthu at gmail.com> wrote:
> Hi Roland,
>  I want to output the pdb file during the simulation. (before every
> integration step). It need not be PDB also, as long as I can figure out
> coordinates of few atoms.
> Just to be clear, are you suggesting nstxtcout to be 1 and using trajconv to
> always read the last frame? Wouldnt that blow up the xtc file ? I just want
> the current co-ordinates of the system, need not have the past ones stored.

doesn't gromacs support the "interactive MD" protocol to hook
up simulations over a TCP socket to VMD?

writing and particularly reading text mode files is a very
expensive operation. using a procedure that communicates
binary information and avoiding writing it to a file as well
seems to be a much more efficient way to process the data.
it would be even more efficient, if you could limit the number
of atoms to be communicated to a small group.

i have done similar things with other MD codes and it
worked pretty well and quite efficient.

> And also these simulations are going to be simultaneous simulations, -multi
> option, would that change your advice about changing the code ?

for IMD, you'd only need to open a different TCP port for each replica,
e.g. just increment the base port number with the replica index.


> Thanks
> Santhosh
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Dr. Axel Kohlmeyer    akohlmey at gmail.com

Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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