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
>>>>>> ==============================================
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>
>>>
>>> _______________________________________________
>>> 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
>>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Adrian E. Roitberg
Full Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 24 2011 - 03:30:03 PDT
