Thank you for your responses.
Regards.
Sonia Ziada
PhD student in molecular modelling and chemoinformatics.
ICOA laboratory, Orléans, France.
2016-09-08 15:26 GMT+02:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> the reason that you did not receive a response may be that there is not
> support for this in the standard code, and you would need to modify the
> code to send this data to a separate file. There is not support for opening
> files for each type of number calculated during MD.
>
>
> On Thu, Sep 8, 2016 at 9:11 AM, Sonia Ziada <sonia.ziada.gmail.com> wrote:
>
> > Dear amber users,
> >
> > Can you help me PLEASE on that topic : I am doing targeted moelcular
> > dynamics (TMD), and i can not find a way to redirect output information,
> > such as the current RMSD (=reaction coordinate in TMD), in an output
> file.
> > I know that it is possible in Umbrella sampling for the distance/angle
> > reaction coordinate using DISANG, DUMPREQ and DUMPAVE options. But I did
> > not find a way to do it in TMD to save the RMSD reaction coordinate. So
> > currently I am retrieving the RMSD from the mdout file (ntpr option),
> which
> > makes my calculation very time consuming because I have to save it much
> > more frequently (Moreover TMD is only implemented in sander !!!). Is
> there
> > a way to save the reaction coordinate RMSD in TMD in an independent
> output
> > file ?
> >
> > Thank you very much in advance.
> >
> > Sonia Ziada
> > PhD student in molecular modelling and chemoinformatics.
> > ICOA laboratory, Orléans, France.
> >
> >
> > 2016-09-08 15:10 GMT+02:00 Sonia Ziada <sonia.ziada.gmail.com>:
> >
> > > Thank you for your response.
> > > I sent this question two times to amber.ambermd.org, before sending it
> > to
> > > you, without getting any response. I will re-submit it a third time.
> > > Regards,
> > >
> > >
> > > Sonia Ziada
> > > PhD student in molecular modelling and chemoinformatics.
> > > ICOA laboratory, Orléans, France.
> > >
> > >
> > > 2016-09-08 14:59 GMT+02:00 David A Case <david.case.rutgers.edu>:
> > >
> > >> On Thu, Sep 08, 2016, Sonia Ziada wrote:
> > >> > Dear David,
> > >>
> > >> Please send amber-related questions to the mail reflector,
> > >> amber.ambermd.org,
> > >> and not to me personally. That way, many people can see your question
> > >> and try
> > >> to help, and the answers can help others with similar questions. See
> > >> http://lists.ambermd.org/mailman/listinfo/amber for information on
> how
> > to
> > >> subscribe.
> > >>
> > >> In particular I have never used targetted MD myself.
> > >>
> > >> ...dac
> > >>
> > >> --
> > >>
> > >> ====================================================================
> > >> David A. Case | david.case.rutgers.edu
> > >> Dept. of Chemistry & Chemical Biology |
> > >> Rutgers University | office: +1-848-445-5885
> > >> 174 Frelinghuysen Road, Rm. 208b | cell: +1-609-751-8668
> > >> Piscataway, NJ 08854 USA | http://casegroup.rutgers.edu
> > >> ====================================================================
> > >>
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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Received on Thu Sep 08 2016 - 07:00:02 PDT
