I think it's a better aprox. for our lab. Nevertheless, I've been
reading the manual and i have a question. Can LES program give me an
approach to my problem, this is, give to the ligand a temperature
different to the system one?
Fernando
On Fri, 17 Jun 2011 19:55:46 -0600, Jason Swails
<jason.swails.gmail.com> wrote:
> 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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>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > 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
>> ==============================================
>>
>> _______________________________________________
>> AMBER mailing list
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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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Received on Wed Jun 22 2011 - 05:30:07 PDT
