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 Barto¹, 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 - 03:30:02 PST
