[gmx-users] Pressure negative after NVT simulation
Alif M Latif
prism_dead at yahoo.com
Mon Mar 31 05:31:20 CEST 2008
Dear GROMACS users and developers,
I am running MD simulation of lipid self-assembly with total of 53 molecules in a 1000 nm3 cubic simulation box with spc216 as the solvent. After minimization i ran constant NPT MD equilibration up to 1 ns (just to make sure) for the system to have suitable volume and density before running with NVT. After the equilibration, i observed the potential energy and it looked fine. So i took the volume of the equilibration trajectory which then was 1025.51 nm3 as my new box volume. Then i ran 5ns of constant NVT MD simulation. After simulation i checked the pressure of the system throughout the simulation and found that the average pressure of the system from g_energy was -12.7856 bar. The xvg file demonstrated that the pressure fluctuate very high from about 100 to -100 troughout 5 ns. I am still not familiar with this situation but i believe that negative value of pressure is not a good thing. Can anyone kindly help me tell what's wrong with my simulation?
Suggestion and comments are greatly appreciated. Thank You.
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia
43400 UPM Serdang, Selangor,
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