On Thu, Nov 17, 2022, Reim, Thorben via AMBER wrote:
>
>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.
>
>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
What you describe looks entirely reasonable to me. When you switch to
consant pressure, there is a sudden increase in volume (decrease in
density), since the initial pressure is quite high. This in turn will
affect both potential and kinetic energies (kinetic indirectly, since the
potential energy changes.)
It will then take a while for the thermostat to re-equilibrate the temperature
to the target value.
....dac
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Received on Thu Nov 17 2022 - 13:00:02 PST
