Hi Sinjini,
well, do your box dimensions change 'too much'? Note that the density can
still be perfectly ok, but the system maybe drifts into a slab like shape
because x,y and z can vary independently of each other with ntp=2. Have you
checked plots of your a,b and c box vectors over the simulation? I seem to
recall a mailing list discussion that suggested very long (by the standards
of back then, so many nanoseconds) simulations of membrane systems can run
into the issue of the box deforming too much. This is a random drift, so
your simulation may still be perfectly converged until you run into PBC
artefacts. Maybe using semiisotropic pressure scaling ntp=3 (vary z alone
and xy together) works better here? This option requires surface tension to
be on, but I think you can switch on csurften but still set gamme_ten to
zero.
Kind Regards,
Thomas
On Fri, Jan 10, 2025 at 12:05 PM Bhattacharjee, Sinjini via AMBER <
amber.ambermd.org> wrote:
> **Warning** The sender address ("Bhattacharjee, Sinjini via AMBER" ) can
> not be verified, sender email address could be spoofed. Please take care to
> proceed.
> 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>
> ---
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 06/OG07
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Fri Jan 10 2025 - 03:30:03 PST
