Dear Amber users,
I am performing a production run on a membrane protein system using Amber20. My system is perfectly equilibrated at 303K and I used a gamma_ln = 5 for the Langevin thermostat, for the equilibration step.
But when I switch to gamma_ln=1 for the production run, I get the following error message and the simulation stops even though there is nothing wrong with the density.
Is there a way to bypass this error?
Also, my other question would be does the gamma_ln value affect the MD results ?
ERROR: Calculation halted. Periodic box dimensions have changed too much
from their initial values.
……..
Alternatively you can run with the CPU code until the density has converged and then switch back to the GPU code.
This is my input for MD:
NPT 303K
&cntrl
imin=0,
ntx=5, ! Positions and velocities read formatted
irest=1, ! Restart calculation
ntc=2,
ntf=2,
tol=0.0000001,
nstlim=9730000, ! Number of MD steps
ntt=3,
gamma_ln=1.0,
ig=-1,
ntpr=10000,
ntwr=5000,
ntwx=5000,
dt=0.002,
ntb=2, ! Constant pressure periodic boundary conditions
ntp=2, ! Anisotropic pressure coupling
taup=2.0, ! Pressure relaxation time (ps)
temp0=303.0,
cut=10.0,
ioutfm=1,
ntxo=2,
&end
/
Thanks for your help!
—
Sinjini Bhattacharjee, PhD (she/her)
Department of Molecular Theory and Spectroscopy
Max-Planck-Institut für Kohlenforschung
45470 Mülheim (Ruhr), Germany
email: bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de>
---
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 10 2025 - 03:30:02 PST
