[gmx-users] water density

[Christopher Neale]

I am fairly confused about what you want to obtain and what you have done, but is it possible that you simply have not turned on pressure coupling? General procedure even if you eventually want to do constant volume simulation is to do some equilibration with constant pressure to get densities correct.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Alexander Alexander <alexanderwien2k at gmail.com>
Sent: 13 June 2016 10:07:32
To: gmx-users at gromacs.org
Subject: [gmx-users] water density

Dear gromacs user,

I have a solid surface with TIP3P water on top of it in the vacuum part. I
am expecting to get the density of bulk TIP3P water (987 +/- 4.0 kg/m^3)
far from the surface in the middle of vacuum part, but, I always get
something around 895-905 kg/m^3 in spite of high equilibrating the system ,
more than 11 ns.
I can get the desired water density in a box with size as big as the vacuum
part including only water.
I know that I should increase the number of water, but "gmx solvate -maxsol
..." does not let me add water more than a specific number of maxsol into
vacuum part on top of the surface. I tried to deceive it by adding more
water in a bigger size box (in Z direction) and then reducing the size
after minimization, but then the SETTEL problem came up.

Any suggestion would be highly appreciated.

Best regards,
Alex
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