[gmx-users] Coarse-grained simulation with MARTINI

[XAvier Periole]

On Dec 14, 2010, at 7:29, samio <u940257 at oz.nthu.edu.tw> wrote:

> Hello
> 
> I am trying to perform a CG simulation on the solvated protein but there is one question that I would like to ask for suggestion. The problem is: the volume of the periodic box varied a lot depending on the Van der Waals distance of the CG water molecule.
> 
> I guess the volume variation is because of the system needs to relax to the correct density, since the number of water molecule is depending on the Van der Waals distance. Is it reasonable if I start the simulation after the volume become stable under position restraint? 
Yes it is. 

You may also want to tune the vdW radius you use in genbox to minimize the equilibration. More accurate the number, the quicker the equilibration. 
> 
> Thanks in advance for reading this post.
> 
> --
> 
> Kuang-Yu Chang
> Institute of Bioinformatic and Structural Biology 
> National Tsin Hua University
> 101, section 2, Kuang-Fu Road,
> Hsinchu 30013
> Taiwan
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