Re: CGMD timestep

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Dec 08 2008 - 12:11:54 CST

On 12/8/08, BIN ZHANG <zhngbn_at_gmail.com> wrote:
> If I were correct, NAMD only use the MARTINI FF for Coarse Grained
> lipid and water, and it has its only CG protein model. So for your
> question, I'm not really sure(that's why I post on the list. :-) )

..and i keep repeating myself. the force field parameters and
the MD code are two _different_ entities.

_you_ have to convince yourself that the parameters _you_ use are
working "good enough" for your purposes. the problem is that we are
not working with absolute truths here, but approximations. and an
approximation that may be a good one for one problem, may be a
not so good one for the next.

the best way to convince yourself, is to make tests with small(er)
subsystems and find out, if you can reproduce properties that you
need to represent well. in CG modelling, poeple take much more
liberties, but that means that there is less transferability. you just
have to know what you are doing. i am a bit old-fashioned and thus
personally would not be comfortable using a parameter set where the
error from using a very large time step is compensated through the
parametrization. but then again, since CG modeling is approximate,
it is a legitimate choice that people make, provided they look at
properties that are not affected by this approximation.

> In their origin RBCG paper, 25fs is used for their protein-lipid
> system, but 15fs is used in another application paper.

see above for my view on these issues and again. the fastest
motion in the system _does_ determine how large a time step
you can choose, but keep in mind that with a langevin thermostat
you add a friction term the size of which has an impact on the
speed of particles. so you have to make choices every where and
you have to justify them in some way.

cheers,
   axel.

> Bin
>
>
>
> On Dec 8, 2008, at 9:37 AM, Axel Kohlmeyer wrote:
>
>> yes.
>>
>> but in how far is this affected by the MD code you are using?
>>
>> axel.
>>
>> On 12/8/08, BIN ZHANG <zhngbn_at_gmail.com> wrote:
>>> Hi, Axel
>>>
>>> Maybe I understood it wrongly, but it says here
>>>
>>> "
>>> In a all-atom FF you assume the free energy surface the FF describes
>>> is actually exact and the smaller the time step the more accurate you
>>> are. You then try to increase the time step to be able to sample bit
>>> more and increase your statistics.
>>> "
>>> And that's normally what we think.
>>> But for the CG FF:
>>> "
>>> Given the CG force field (set of parameters) and thus the potential
>>> energy surface of the system, the way you are going to explore this
>>> particular surface is actually depending on many parameters and time
>>> step is part of them. A reduction of the time step would favor the
>>> states of the system with the lower potential energy. This is
>>> equivalent to play with the temperature. This is also true for the
>>> cutoff -do not modify the cutoff- it is part of the force field.
>>> Increasing the cutoff will not make your run more accurate but at the
>>> contrary alter the balance of the different terms.
>>> "
>>>
>>> Bin
>>>
>>>
>>>
>>> On Dec 8, 2008, at 9:19 AM, Axel Kohlmeyer wrote:
>>>
>>>> bin,
>>>>
>>>> if i'd read the link, what would it help you?
>>>>
>>>> figuring out what is a proper time step for a given
>>>> problem is an _elementary_ skill in doing MD, so you'll
>>>> have to convince yourself that you make the right choice.
>>>>
>>>> cheers,
>>>> axel.
>>>>
>>>>
>>>> On 12/8/08, BIN ZHANG <zhngbn_at_gmail.com> wrote:
>>>>> Hi, Axel:
>>>>>
>>>>> I appreciate your comment, but I would be more appreciative if you
>>>>> would read the link.
>>>>> Thanks.
>>>>>
>>>>> Bin
>>>>>
>>>>>
>>>>>
>>>>> On Dec 8, 2008, at 1:26 AM, Axel Kohlmeyer wrote:
>>>>>
>>>>>> On 12/7/08, BIN ZHANG <zhngbn_at_gmail.com> wrote:
>>>>>>> Dear all:
>>>>>>>
>>>>>>> I just find this link abut MARTINI forcefield (
>>>>>>> http://wiki.gromacs.org/index.php/Coarse_Grained_Force_Field
>>>>>>> ), which says "The force field has been parametrized to be
>>>>>>> valid in
>>>>>>> the range 0.02/0.04 ps."
>>>>>>> Does this argument also hold for NAMD?
>>>>>>
>>>>>> dear bin,
>>>>>>
>>>>>> please refer to your favorate text book on MD and
>>>>>> see that the maximum allowed time step is determined
>>>>>> by the fastest motions in your system (i.e. mass of particles
>>>>>> and stiffness of interactions), the magnitude of error you
>>>>>> are willing to accept and the stability of the time integration
>>>>>> algorithm employed. except for the last item everything does
>>>>>> not depend on the MD implementation and since practically
>>>>>> all widely used classical MD codes employ one over the Verlet
>>>>>> variants, also the last point is in practice irrelevant.
>>>>>> with that in mind, you should be able to answer your question
>>>>>> by yourself.
>>>>>>
>>>>>> cheers,
>>>>>> axel.
>>>>>>
>>>>>>> Thanks a lot.
>>>>>>>
>>>>>>> Bin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -------------------------------------------------------------
>>>>>>> The tree of liberty must be refreshed from time to time with the
>>>>>>> blood
>>>>>>> of patriots and tyrants.
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ==================================================================
>>>>>> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
>>>>>> www.cmm.upenn.edu
>>>>>> Center for Molecular Modeling -- University of Pennsylvania
>>>>>> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
>>>>>> 19104-6323
>>>>>> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
>>>>>> 1-215-898-5425
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ==================================================================
>>>>>> If you make something idiot-proof, the universe creates a better
>>>>>> idiot.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------------
>>>>> The tree of liberty must be refreshed from time to time with the
>>>>> blood
>>>>> of patriots and tyrants.
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> =
>>>> =
>>>> =
>>>> ====================================================================
>>>> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
>>>> www.cmm.upenn.edu
>>>> Center for Molecular Modeling -- University of Pennsylvania
>>>> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
>>>> 19104-6323
>>>> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
>>>> 1-215-898-5425
>>>> =
>>>> =
>>>> =
>>>> ====================================================================
>>>> If you make something idiot-proof, the universe creates a better
>>>> idiot.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------------
>>> The tree of liberty must be refreshed from time to time with the
>>> blood
>>> of patriots and tyrants.
>>>
>>>
>>
>>
>> --
>> =
>> ======================================================================
>> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
>> www.cmm.upenn.edu
>> Center for Molecular Modeling -- University of Pennsylvania
>> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
>> 19104-6323
>> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
>> =
>> ======================================================================
>> If you make something idiot-proof, the universe creates a better
>> idiot.
>
>
>
>
>
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>
>
> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the blood
> of patriots and tyrants.
>
>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

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