[gmx-users] Coarse-grained simulation with MARTINI

[samio]

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?

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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