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

[Berk Hess]

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.
>>_______________________________________________
>>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!
>>Please don't post (un)subscribe requests to the list. Use the www 
>>interface or send it to gmx-users-request at gromacs.org.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>-----------------------------------------------------
>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!
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Play online games with your friends with Messenger 
http://www.join.msn.com/messenger/overview