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
> >> ====================================================================
> >>
> >
> >
> _______________________________________________
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>
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Received on Thu Sep 08 2016 - 06:30:03 PDT
