[gmx-users] Re: abnormal flip-flop whenembeddingcholesterol into DOPC using

[Berk Hess]

Hi,

If the differences are in that order of magnitude, you might indeed be able
to compensate integration errors in the force field in a relatively 
controlled way.
I will be in Groningen next week, so there I can discuss these issues in 
detail.

Berk.


>From: "Xavier Periole" <X.Periole at rug.nl>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Re: abnormal flip-flop whenembeddingcholesterol 
>into	DOPC using
>Date: Thu, 06 Dec 2007 19:33:36 +0100
>
>
>Hi Berk,
>
>the effect on the partitioning free energy of the beads is up to ~5%
>when going from 40 to 5 fs time step. This was reported in the MARTINI
>paper. Although the effect is small it is present and it is better
>that users know and use the time step used for the parametrization
>in order to avoid altering the properties of the FF and thus the
>description of the system. Although the effect is marginal we are
>dealing with multi-microsecond simulations and small differences
>could be observed.
>
>It is important to keep in mind that the MARTINI model is a Coarse Grain
>approach and thus: "considering the inherent approximative
>nature of the underlying CG potentials, this is not problematic
>per se as long as the time step used in simulations does not differ
>too much from the time step used for the parametrization."
>Quote from the MARTINI paper.
>
>XAvier
>
>On Thu, 06 Dec 2007 16:52:37 +0100
>  "Berk Hess" <gmx3 at hotmail.com> wrote:
>>Hi,
>>
>>I hope that what you are saying is not true.
>>The timestep should not influence your results, unless you make it so 
>>large
>>that it causes significant inaccuracies in your results.
>>If you say you should not use a smaller time step, that would mean the 
>>force field
>>is set up such that it purposely compensates for integration errors.
>>I don't think one could do that in an accurate and controlled manner.
>>
>>Berk.
>>
>>
>>>From: "Xavier Periole" <X.Periole at rug.nl>
>>>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>Subject: Re: [gmx-users] Re: abnormal flip-flop when 
>>>embeddingcholesterol	into DOPC using CG
>>>Date: Thu, 06 Dec 2007 13:14:10 +0100
>>>
>>>
>>>Dear Ran,
>>>
>>>The reasoning of a CG-FF is a bit different than for an all-atom FF.
>>>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.
>>>
>>>In the case of a CG FF, and especially for the MARTINI one, you use
>>>an approximated potential energy surface of the all-atom one (with a
>>>strong smoothing of the surface) but you should reproduce all-atom and
>>>experimental observables. 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.
>>>
>>>In summary: The time step determines the balance between enthalpy
>>>and entropy. The smaller the time step the smaller the entropy. The
>>>force field as been parametrized to be valid in the range 0.02/0.04 ps.
>>>
>>>One exemple: the partitioning (used to parametrize the beads in the
>>>MARTINI FF) is dependent on the time step. A small time step would
>>>favor the state where the enthalpy is lower.
>>>
>>>Best
>>>XAvier
>>>
>>>>>One other thing. In the CG FF the time step is considered as part of 
>>>>>the
>>>>>force field. Meaning that you should not play with it too much.
>>>>>0.04-0.02 ps is the actual range where the force field is considered
>>>>>to reproduce experimental values of various quantities used for
>>>>>paraameterization of the FF. Outside this range you change the balance
>>>>>between the different terms and thus would alter the quality of the FF.
>>>>Can you elaborate on this a bit? Surely if one changes the temperature,
>>>>pressure, compressibility, threshold distances etc., one doesn't
>>>>necessarily reproduces the experimental results. Too long timesteps may
>>>>also cause a problem. But why would it be wrong to use a shorter time
>>>>step here?
>>>>
>>>>Ran.
>>>>_______________________________________________
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>>>
>>>-----------------------------------------------------
>>>XAvier Periole - PhD
>>>
>>>NMR & Molecular Dynamics Group
>>>University of Groningen
>>>The Netherlands
>>>http://md.chem.rug.nl/~periole
>>>-----------------------------------------------------
>>>_______________________________________________
>>>gmx-users mailing list    gmx-users at gromacs.org
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
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>>
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>
>-----------------------------------------------------
>XAvier Periole - PhD
>
>NMR & Molecular Dynamics Group
>University of Groningen
>The Netherlands
>http://md.chem.rug.nl/~periole
>-----------------------------------------------------
>_______________________________________________
>gmx-users mailing list    gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/search before posting!
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