On 1/5/13 3:53 PM, Yutian Yang wrote:
Hi all,
I have some problems with the pressure of my system. When I try to run
equilibrium systems (NVT or NPT), I have got large pressure fluctuations (2 or
3 orders higher than average value). When I apply shear to the system, the
pressure of the system increases with the increasing shear rate, which is
normal, but the fluctuations don't change much. The following is the actual
results for a (5nm)^3 box. Are these results normal? Or are there any problems
with the simulations?
Pressure values almost always have huge fluctuations associated with them.
http://www.gromacs.org/Documentation/Terminology/Pressure
-Justin
Thank you so much!
NVT:
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Pressure 71.1917 1.9 103.261 -3.68971 (bar)
Pres-XX 71.1268 1.7 150.31 -3.3972 (bar)
Pres-XY -0.106214 0.37 94.633 0.382172 (bar)
Pres-XZ 0.182851 0.13 94.6965 0.0525603 (bar)
Pres-YX -0.106214 0.37 94.633 0.382172 (bar)
Pres-YY 70.7725 2.1 150.345 -3.08484 (bar)
Pres-YZ 0.149167 0.42 94.5955 1.01412 (bar)
Pres-ZX 0.182851 0.13 94.6965 0.05256 (bar)
Pres-ZY 0.149166 0.42 94.5955 1.01412 (bar)
Pres-ZZ 71.6759 2.2 150.227 -4.58708 (bar)
NPT:
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Pressure 0.975026 0.042 89.3802 0.0580066 (bar)
Pres-XX 1.93729 0.43 139.974 -0.727682 (bar)
Pres-XY -0.938744 0.65 93.4597 2.31599 (bar)
Pres-XZ 0.00540739 0.51 93.5049 -2.21079 (bar)
Pres-YX -0.938744 0.65 93.4597 2.31599 (bar)
Pres-YY -0.75967 0.61 140.338 0.703514 (bar)
Pres-YZ -0.0475309 0.62 93.4529 0.234715 (bar)
Pres-ZX 0.00540704 0.51 93.5049 -2.21079 (bar)
Pres-ZY -0.0475311 0.62 93.4529 0.234714 (bar)
Pres-ZZ 1.74746 0.47 140.156 0.198188 (bar)
Shear rate 0.04 1/ns
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Pressure 68.7197 0.83 103.185 3.16213 (bar)
Pres-XX 67.9871 0.96 150.379 4.90957 (bar)
Pres-XY -1.87457 0.26 94.606 1.52909 (bar)
Pres-XZ -0.14688 0.24 94.5825 -0.986185 (bar)
Pres-YX -1.87457 0.26 94.606 1.52909 (bar)
Pres-YY 68.7435 0.94 150.28 1.77856 (bar)
Pres-YZ 0.406456 0.32 94.5859 -1.08897 (bar)
Pres-ZX -0.14688 0.24 94.5825 -0.986184 (bar)
Pres-ZY 0.406456 0.32 94.5859 -1.08897 (bar)
Pres-ZZ 69.4285 0.73 150.176 2.79824 (bar)
Shear rate 52.3 1/ns
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Pressure 244.394 1.3 116.824 0.743594 (bar)
Pres-XX -107.921 2.5 198.609 -6.31786 (bar)
Pres-XY -386.103 0.32 101.948 -1.42629 (bar)
Pres-XZ -0.0737284 0.46 100.128 2.03768 (bar)
Pres-YX -386.103 0.32 101.948 -1.42629 (bar)
Pres-YY 459.455 1.1 154.569 3.95874 (bar)
Pres-YZ -0.125439 0.17 95.0531 0.28234 (bar)
Pres-ZX -0.0737286 0.46 100.128 2.03768 (bar)
Pres-ZY -0.125439 0.17 95.0531 0.28234 (bar)
Pres-ZZ 381.649 1.2 152.955 4.5899 (bar)
Yutian
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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