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
Received on Thu Sep 08 2016 - 06:30:02 PDT
