This is what I supposed. Thank you, Adrian
Fernando
On Fri, 24 Jun 2011 12:25:44 +0200, Adrian Roitberg
<roitberg.qtp.ufl.edu> wrote:
> Dear Fernando:
>
> What Karplus calls "Multicopy enhanced sampling molecular dynamics
> (MCES)" in that paper is exactly LES (Locally Enhanced Sampling). So,
> if
> you want to do what he did, LES is the way to go.
>
> Adrian
>
>
> On 6/24/11 9:10 AM, Fernando Martín García wrote:
>> Thank you all for you answers. Anyway, I'll try LES way. Maybe
>> I've not
>> explain very well. The idea we have in our lab is to apply the
>> temperature not to the whole ligand, but only to a phosphate
>> coming from
>> a GTP and that is independent of it, i mean, GDP+PHOS. We took
>> this idea
>> from the next paper:
>>
>> http://www.sciencedirect.com/science/article/pii/S0969212610000717
>>
>> Again, thank you for your answers and time
>>
>> Fernando
>>
>> On Wed, 22 Jun 2011 14:51:03 -0400, Carlos Simmerling
>> <carlos.simmerling.gmail.com> wrote:
>>> yes this is in fact the main issue. you can't effectively do this,
>>> and
>>> trying to do it violates any ensemble I know about, so it's
>>> probably
>>> only useful as a search tool. For that, though, it can be quite
>>> effective.
>>>
>>> On Wed, Jun 22, 2011 at 2:47 PM, Sergio R Aragon<aragons.sfsu.edu>
>>> wrote:
>>>> Hello Fernando, Carlos and others,
>>>>
>>>> I've been thinking about the idea of having one part of a system a
>>>> different temperature than another part of the system in a
>>>> simulation.
>>>> David Case is correct that just changing the masses of the atoms
>>>> will not work, for the temperature is a measure of the average
>>>> kinetic
>>>> energy, and that depends on both mass and velocities. There is
>>>> another fundamental problem with the idea, however, because
>>>> presumably
>>>> you will not eliminate all coupling of the ligand to the rest of
>>>> the
>>>> system. This implies that if you generate a separate thermostat
>>>> for
>>>> the ligand part and keep its temperature higher, then energy will
>>>> be
>>>> transferred, via the interaction couplings with the rest of the
>>>> system, to other parts of the molecule and eventually to the
>>>> solvent.
>>>> Thus the solvent thermostat will have to be removing energy that
>>>> gets input into the ligand via its own thermostat. This is not an
>>>> equilibrium system, but a steady state one in which there is a
>>>> gradient in temperature in the system. The sustained temperature
>>>> gradient will cause other effects such as mass transport, and it
>>>> may
>>>> take a while of simulation before the steady state gets achieved.
>>>> Then, what kind of an ensemble is suitable for interpreting the
>>>> data?
>>>> Some serious thought about the fundamentals appears to be
>>>> warranted
>>>> before proceeding with this idea.
>>>>
>>>> Cheers,
>>>>
>>>> Sergio Aragon
>>>> SFSU
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
>>>> Sent: Wednesday, June 22, 2011 10:58 AM
>>>> To: AMBER Mailing List
>>>> Subject: Re: [AMBER] System temperature
>>>>
>>>> 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
>>>>>>> ==============================================
>>>>>>>
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>>>>>>> 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
>>>>> ==============================================
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
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--
==============================================
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 Fri Jun 24 2011 - 04:00:03 PDT
