> my calculation is much more time consuming because I have to save it
much more frequently
Someone could add a feature whereby values get cached in memory for
numerous mdout write cycles instead of being written to file, then at
some greater interval the finer-grain info could be written.
Bill
On 9/8/16 7:45 AM, Sonia Ziada wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Sep 08 2016 - 10:30:02 PDT
