can you share your leap input, and which version of AmberTools you are
using? is it fully up to date with patches?
if you suspect HMR, did you try a run without HMR?
On Mon, Nov 21, 2022 at 6:21 AM Piia Bartos via AMBER <amber.ambermd.org>
wrote:
> Hi Amber people,
>
> I tried to test the new OPC3-pol water model with my protein system.
>
> It seems to be incompatible with some of my simulation parameter, as the
> simulations with the OPC3-pol water appear to be "frozen", where atoms
> remain almost still thorough the simulation (500 ns). The same production
> script works fine for OPC water model. Any ideas what I need to change? The
> issue might be with the Parmed, HMR and using 4fs timestep, but I think I
> built the system correctly...
>
> Here is the production script:
> # 500 ns production Langevin thermostat + Monte carlo barostat dynamics
> &cntrl
> imin=0,
> irest=1, ntx=5,
> ntpr=25000, ntwx=25000, ntwr=25000,
> ntb=2, barostat=2, cut=10, iwrap=1,
>
> nstlim=125000000, nscm=0, dt=0.004,
> ntt=3, gamma_ln = 1, ig=-1, temp0=310, tempi=310,
> ntp=1,
> ntc=2, ntf=2,
> ioutfm=1,
> /
> &ewald
> netfrc = 0,
> skin_permit = 0.75,
> &end
> /
>
> Cheers,
> Piia
>
> --
> Piia Bartoš, Ph.D. (Pharmacy)
> Project Researcher
>
> University of Eastern Finland | UEF | School of Pharmacy
> Kuopio Campus | Canthia
> Yliopistonranta 1 C | P.O. BOX 1627 | 70211 Kuopio
> +358 50 548 8376 | piia.bartos.uef.fi<mailto:piia.bartos.uef.fi>
>
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Received on Mon Nov 21 2022 - 08:30:02 PST
