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
>>> ====================================================================
>>>
>>
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> 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 - 08:00:02 PDT
