Hi,
I am trying to simulate an RNA-protein complex where I need the parameters for 5' terminal phosphates. I know of terminal_monophosphate.lib and terminalphos.LJbb-RNA.lib, which should contain these parameters for the corresponding force fields.
The problem is that these simulations crash because of the phosphates become unstable, after a few ns of the production run. My default settings include ff19SB for protein, OL3 for RNA and OPC water model, and HMR to use 4fs timestep.
Things I have tried:
1. Removing terminal phosphates leads to stable simulations so the system is otherwise fine.
2. Longer equilibration -> still crashes.
3. Not using hydrogen mass repartitioning and 4fs timestep, but a timestep of 2fs -> still crashes.
4. Using the OHE residue as described in Amber manual (3.2.3) and not -> still crashes.
5. Changing the RNA force field to RNA.LJbb -> still crashes.
I am seeing some MC barostat warnings (MC Barostat: Decreasing size of volume moves) in the production run before the crash. Could it be that the parameters of these terminal phosphates are somehow incompatible with the MC barostat?
I would appreciate any help. I included my production script below.
Cheers,
Piia Bartos
Prod.in:
# 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
/
--
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 Wed Feb 22 2023 - 02:00:03 PST
