[gmx-users] Paradox in .mdp parameter value between Justin's tutorial and martini's one

[Justin Lemkul]

On 6/9/16 2:37 AM, khourshaeishargh at mech.sharif.ir wrote:
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> 	Dear Gromacs user
>
>
> 	I&#39;m currently working with Coarse grain martini forcefield, but
> before that I&#39;ve used all atom simulation. in the below suggested
> .mdp file [1] , as you notice the recommended value for tau-t with
> V-rescale is 1 and the recommended value for tau-p with Parrinello-Rahman
> is 12 but as you have remembered in Justin&#39;s tutorial this value are
> set to 0.1 and 5 in order. beside, the compressibility value in
> Justin&#39;s tutorial for DPPC and water is set to 4.5e-5 but in the
> below .mdp file it is set to 3e-4. also Justin has answered to a person
> that these value are not forcefield dependence at all. so is there any
> paradox or not ? I really appreciate it if you give a direct answer to
> me.
>

The energy surfaces of a coarse-grained system and an atomistic one are very 
different.  You're comparing apples and oranges here, but in general, no, there 
is no paradox and nothing abnormal about this.  There are no hard and fast rules 
for coupling times (at least, not that I'm aware, as long as people aren't 
choosing absurdly short or long times).

-Justin

>
> 	sincerely, Ali
>
>
> 	[1] :
> http://md.chem.rug.nl/images/parameters/exampleMDP/martini_v2.x_new-rf.mdp
>
> ==================
>
> Ali khourshaei shargh (khourshaeishargh at mech.sharif.ir)
>
> Department of Mechanical Engineering
>
> Sharif University of Technology, Tehran, Iran
>
>
> 	
>
> 	�
>
> 	�
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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