normal Martini tutorials: Free energy techniques - Free sampling - compressibility

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1 week 4 days ago #7485 by yogi@martini
yogi@martini created the topic: Martini tutorials: Free energy techniques - Free sampling - compressibility
Hello experts,

In the eq.mdp file, pressure is scaled only in z direction by setting compressibility to zero for x/y plane. Are we doing something unphysical here?
The pressure tensor in XX and YY is coming out to be -86.9396 and -94.5327 bar respectively while in ZZ it is ~ 1bar. How we are making sure that the system is true ensemble? since we are using it to calculate a partition coefficient - a physical quantity.

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1 week 4 days ago #7489 by bart
bart replied the topic: Martini tutorials: Free energy techniques - Free sampling - compressibility
At the moment I couldn't quickly write down the proof of it remaining a true ensemble, but what it boils down to, is that the water has a different internal pressure, than the membrane. At least thats how I always looked at it.

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1 week 3 days ago #7490 by yogi@martini
yogi@martini replied the topic: Martini tutorials: Free energy techniques - Free sampling - compressibility
Dear Bart, thanks for the reply.

But here the scaling is done for the system (membrane+water), and freedom is given for direction (x/y or z) in which to scale, hence whichever direction we choose to scale, it's going to effect whole system. The gromacs manual has discussed it very briefly, which is difficult to understand. Do you have any documentation/manual/paper where you people have discussed these things. Definitely lot of brain storming had been gone into making this setting. Any suggestion will be helpful.

Thanks a lot
Yogi

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