Another idea, though it may require careful thinking about, is to 'trick'
the system into heating different atoms differently simply by changing the
masses of certain atoms (for instance, make them heavier if you want to
lower the temperature of that part, etc.). None of the forces should depend
on the masses of adjacent particles (the amber force field doesn't take
gravitational effects into consideration ;)). Of course you'd have to
calculate by how much to increase (or decrease) the masses to reach the
desired "target" temperature (or effective temperature).
Keep in mind, whether you take the T approach as Ross suggested (but bear in
mind that you may have to adjust thermostat behavior in addition to setvel
that in dynlib.f, since that will only affect the initial velocities).
I may be corrected in this advice if it turns out that I'm missing something
critical.
HTH,
Jason
2011/6/16 Fernando Martín García <fmgarcia.cbm.uam.es>
> Thank you for the answer, but i have a question: is that means i have
> to create a tempi and tempi_atomselect in my input files to specify the
> temperatures?
>
> Thanks
>
> Fer
>
> On Wed, 15 Jun 2011 16:00:04 -0700, "Ross Walker"
> <ross.rosswalker.co.uk> wrote:
> > 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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> >
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> ==============================================
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 17 2011 - 19:00:03 PDT
