[gmx-users] 0 +- 0.5 bar ok?

Johnny Lu johnny.lu128 at gmail.com
Mon Dec 15 17:01:02 CET 2014


Are these pressures acceptable for reviewers? (I haven't submit anything to
journals before). What would be different from a simulation with a truly 1
bar average pressure?

System 1: NVT simulation gives an 0.0 +- 0.5 bar average pressure over
600ns with 2 fs timestep. When I averaged the 2nd half of the simulation,
it gives -0.3 +- 0.5 bar average pressure over 300 ns. The system has 9K
water molecules, 3 Cl- ions, and 173 amino acid residues (2598 atoms).

System 2: Another simulation that i did was an alanine dipeptide simulation
with a 5.4 +- 0.2 bar pressure over 250 ns. The last 150 ns gives an
average pressure of 5.6 +- 0.2 bar. The system has 8k water molecules and
32 peptide atoms.

Thank you again.

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