does the issue occur when you maintain the simulation parameters from the
prior run? (same restraints and refc, and so on)
On Thu, Nov 17, 2022 at 6:46 AM Reim, Thorben via AMBER <amber.ambermd.org>
wrote:
> 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 - 07:30:03 PST
