Hi Fernando,
Unfortunately there is no 'automated' way to do this, however, it would not be too difficult to code something in.
See the function setvel in dynlib.f. This is called in the case when you are not doing a restart. You can call the atommask function from within here to process a mask of your choice then modify the atoms that come back from the mask within setvel depending on what you want their velocities (and ultimately temperature) to be.
All the best
Ross
> -----Original Message-----
> From: Fernando Martín García [mailto:fmgarcia.cbm.uam.es]
> Sent: Wednesday, June 15, 2011 7:31 AM
> To: amber.ambermd.org
> Subject: [AMBER] System temperature
>
> Dear Amber users:
>
> I have a question about the assignment of temperature of the system:
> is
> there any possibility to assign different temperatures to different
> parts of the system? I mean, for example, give a high temperature to a
> ligand and a "room temperature" to the protein, using two different
> mask
> for the system.
>
> Thanks
>
> --
> ==============================================
> FERNANDO MARTIN GARCIA
> GRUPO DE MODELADO MOLECULAR - LAB 312.1
> CENTRO DE BIOLOGíA MOLECULAR SEVERO OCHOA
> C/ NICOLáS CABRERA, 1.
> CAMPUS UAM. CANTOBLANCO, 28049 MADRID. SPAIN.
> TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
> ==============================================
>
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Received on Wed Jun 15 2011 - 16:30:03 PDT
