Hello Florent,
Thank you very much for your reply. This is what I'm actually doing:
parsing the mdout file to retrieve the RMSD. But as i said in a precedent
email, by this way, my calculation is much more time consuming because I
have to save it much more frequently and because the mdout file does not
contain only RMSD output but also other information etc..
Thank you. Regards.
Sonia Ziada
PhD student in molecular modelling and chemoinformatics.
ICOA laboratory, Orléans, France.
2016-09-08 16:24 GMT+02:00 Florent Barbault <
florent.barbault.univ-paris-diderot.fr>:
> Hi Sonia,
>
> I hope that you are well. In amber output file of a TMD you should find:
>
>
> | RE_POSITION Moving by 1.247552 4.852088 1.442587
>
> NSTEP = 67000 TIME(PS) = 134.000 TEMP(K) = 298.64 PRESS
> = 0.0
> Etot = -1853.3551 EKtot = 3809.9259 EPtot = -5663.2811
> BOND = 972.4198 ANGLE = 2574.7951 DIHED = 3444.8079
> 1-4 NB = 1271.3766 1-4 EEL = 14005.0303 VDWAALS =
> -2647.6700
> EELEC = -22303.7555 EGB = -2980.7260 RESTRAINT =
> 0.4409
> EAMBER (non-restraint) = -5663.7219
> Current RMSD from reference: 3.863
> Current target RMSD: 3.893
> ------------------------------------------------------------
> ------------------
>
> I suggest you these basics command lines:
>
> $ egrep "NSTEP" amberfile.out > nstep.csv
> $ egrep "Current RMSD from" amberfile.out > curr_RMSD.csv
> $ egrep "Curent targ" amberfile.out > curr_target_RMSD.csv
>
> Then open these three files in a spreadsheet (open office for example).
> Remove some columns, copy, paste.... You do what you want.
>
> PS: As you are French, don't forget to change all ' . ' in ' , '
>
> Regards
> Florent
>
> Le 08/09/2016 à 15:11, Sonia Ziada a écrit :
> > 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
>
>
> --
> -------------------------------------------------
> Dr Florent Barbault
> Maitre de conferences / Associate professor
>
> Universite Paris Diderot
> Laboratoire ITODYS
> 15 rue Jean de Baïf, bâtiment Lavoisier
> 75013 Paris FRANCE
> http://florentbarbault.wordpress.com/
> tel : (33) 01-57-27-68-61
> e-mail : florent.barbault.univ-paris-diderot.fr
> -------------------------------------------------
>
>
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Received on Thu Sep 08 2016 - 08:00:03 PDT
