In a simulation of a dipeptide in water ,I have equilibrated using Berendsen pressure coupling using the parameters given in the attached file. Why isn't my pressure reaching the desired pressure of 1bar? What is the significance of err.est. , RMSD, tot-drift values? At what average pressure can I start production run?
Energy Average Err.Est. RMSD Tot-Drift
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Pressure 2.54142 1.6 433.11 -8.84365 (bar)
http://www.gromacs.org/Documentation/Terminology/Pressure
Your average pressure is 2.5 ± 433, which is clearly indistinguishable from 1. This is normal with pressure, which fluctuates very widely.
http://www.gromacs.org/Documentation/Terminology/Pressure
Your average pressure is 2.5 ± 433, which is clearly indistinguishable from 1. This is normal with pressure, which fluctuates very widely.
Err.est is probably calculated as P_avg-P_desired, RMSD is the root mean squared deviation and tot-drift is the total drift over the MD trajectory. The drift is quite substantial and indicates that the system has not reached equilibrium. How long is this traj? When the system is properly equilibrated, there should be no large drift in the total energy, pressure and volume. The avg. pressure should equal the desired value.
My trajectory was 3ns long. Wasn't it enough? Could anyone look over my parameter file (attached in the question) to see what I could possibly be doing wrong?
I couldn't understand Justin's comment as to how 2.5 +/- 433 could be indistinguishable from 1? So how would I judge whether I should go ahead with the production run or not? Say if I have an average of 7bar +/- 500..would that still be okay?
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