yes this should be possible, buy setting the # of copies to 1 for the ligand.
2011/6/22 Fernando Martín García <fmgarcia.cbm.uam.es>:
> 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
>>> >> ==============================================
>>> >>
>>> >> _______________________________________________
>>> >> AMBER mailing list
>>> >> AMBER.ambermd.org
>>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>> >
>>> > _______________________________________________
>>> > 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
>>> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 22 2011 - 11:00:03 PDT
