Dear Amber-Community,
I try to conduct simulations of proteins crystals follwing the amber tutorial (1.8 Simulation of a Protein Crystal). During my equilibration using restraints on all my proteins chains, swiching from NVT (heating phase) to NPT (unit cell volume equilibration) I encounter the issue of a temperature drop right in the beginning of my NPT which needs about 1 ps to get back to my define temperature of 293K.
Attached you will find my mdin files. As refc for the NPT I am using the restrt from my heating, but even without restraints the problem occurs.
This is a extract of the mdout file.
NSTEP = 1 TIME(PS) = 50.002 TEMP(K) = 293.80 PRESS = 1730.0
NSTEP = 51 TIME(PS) = 50.102 TEMP(K) = 285.22 PRESS = 200.3
NSTEP = 101 TIME(PS) = 50.202 TEMP(K) = 287.03 PRESS = 303.0
NSTEP = 151 TIME(PS) = 50.302 TEMP(K) = 286.42 PRESS = 464.9
NSTEP = 201 TIME(PS) = 50.402 TEMP(K) = 287.76 PRESS = 198.0
NSTEP = 251 TIME(PS) = 50.502 TEMP(K) = 288.83 PRESS = 124.9
NSTEP = 301 TIME(PS) = 50.602 TEMP(K) = 289.56 PRESS = -75.6
NSTEP = 351 TIME(PS) = 50.702 TEMP(K) = 290.43 PRESS = -399.1
NSTEP = 401 TIME(PS) = 50.802 TEMP(K) = 290.48 PRESS = 75.2
NSTEP = 451 TIME(PS) = 50.902 TEMP(K) = 293.92 PRESS = 29.3
What am I doing wrong? How can I fix this?
Thanks in advance,
Thorben
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Received on Thu Nov 17 2022 - 04:00:02 PST
