Re: CGMD timestep

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Dec 08 2008 - 11:37:37 CST

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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