Hi gmx users, I am now simulating one protein with solvent, in all atom
forcefield, gromacs official distributed version. The pressure of system
seems to be unreasonable large, and during the whole process, the box keeps
increasing.
Here is how I set up the system,
1. I solvate the proteini use spc216.gro, the log file shows:
Output configuration contains 40990 atoms in 12386 residues
Volume: 412.593 (nm ^3)
Density: 1015.79 g/L
Number of SOL molecules: 13410
2. Then I start to do MD with constrains (40 ps), then MD without
constrains.
The md.log shows pressure keeps decrease, start from 5.79
e+02 until at last to about 3.14e+00, so you can see how large the box size
is enlarged.
However in my setup, what I use for P-coupling is the same:
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
my integral step size is 1fs, so the tau_p = 0.5 ps should be
enough. Also I checked the temperature, it is constant during the MD
process. (303K)
So from these setup process, I think: the density is correct for
solvent water and system; the compressibility is chosen as for standard
water, the ref_p is chosen as 1.0. Why the pressure is so large?
Thank you in advance!
--
Sincerely
=================================
Pan Wu
Graduate Student in Department of Chemistry
Duke University
124 Science Drive
5301 French Family Science Center
Durham, NC 27708
Phone: (919) 660-1583
=================================
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