[gmx-users] REMD, demux after 100 ns per replica

[Andrea Pérez-Villa]

That was exactly what I did! I have edited the line 70 to change the column
6 to 4 (so the column with the step instead of the time) multiplied by the
time step (in my case 0.002 ps) and the printf in the lines 33 and 44.

I think that the script *pl can be edited to be more general, taking into
account the time step and the precision for the printf. I was thinking that
it can be solved if we write a printf specification very high with the aim
to cover the time scale of very long simulations, and adding a line that
reads from the log file or from the user the time step in ps.
I tried just adding in the pl file a couple of lines asking the time step
in ps, so at least you don't need to seek the line 70 and edit it for the
particular time step value. This is the pl file:
https://drive.google.com/file/d/0B2zhJAKVbM97UDdYaGUwUjl5RFU/edit?usp
=sharing

Do you have some other ideas?
Thank you!!
Andrea.










2014-05-02 20:53 GMT+02:00 Christopher Neale <chris.neale at alum.utoronto.ca>:

> Turns out I had to also change the printf specification from %-20g to
> %-20.2f on lines 33 and 44 (the only two places where %-20g appears).
>
> Seems to be working well now, although %-20.2f is not guaranteed to work
> if exchanges are more frequent than 10 fs.
>
> Chris.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> Christopher Neale <chris.neale at alum.utoronto.ca>
> Sent: 02 May 2014 14:28
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] REMD, demux after 100 ns per replica
>
> Dear Andrea:
>
> I can't access your script now that posts have been removed from nabble.
>
> I have tried changing demux.pl line 70
>
> from:
>             $tstep = $log_line[6];
>
> to:
>             $tstep = 0.002 * $log_line[4];
>
>
> where 0.002 is my timestep. Did you do this or something similar?
>
> Thank you,
> Chris.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of aperez <
> a.pervilla at gmail.com>
> Sent: 22 April 2014 12:46
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] REMD, demux after 100 ns per replica
>
> Hi,
>
> I did an extra modification to the *.pl with the aim of being more general
> with the time step.
> I have just added a line that asks the time step.
> Note: I don't know perl, so I apologize for the rustic way how I modified
> the file.
> Thanks,
> Andrea
>
> proof_demux.pl
> <http://gromacs.5086.x6.nabble.com/file/n5016005/proof_demux.pl>
>
> -----
> Andrea Pérez-Villa
> PhD student in Physics and Chemistry of Biological Systems
> SISSA, Italy
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-- 
Andrea Pérez Villa
*"Res non Verba"*