Re: [AMBER] OPC3-pol

From: Piia Bartos via AMBER <amber.ambermd.org>
Date: Tue, 29 Nov 2022 08:42:34 +0000

Hi,

I am using AmberTools22, which was installed on our supercomputer last week along with Amber22 (no issues during installation and/or testing). So it should have all the necessary patches.

I just tested, the HMR is not the issue, similar behavior happens also without it at 2fs timestep.

Here is the tleap:
source leaprc.protein.ff19SB
source leaprc.RNA.OL3
WAT = O3P
source leaprc.water.opc3pol
loadAmberParams frcmod.opc3pol_HMR4fs
loadAmberParams frcmod.ionslm_126_opc

molc = loadPdb "input.pdb"
solvatebox molc OPC3BOX 10.0
addIonsRand molc Na+ 88
addIonsRand molc Cl- 92
saveAmberParm molc structure.prmtop structure.inpcrd
savePdb molc structure.pdb
quit

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>
From: Carlos Simmerling <carlos.simmerling.gmail.com<mailto:carlos.simmerling.gmail.com>>
Sent: maanantai 21. marraskuuta 2022 18.13
To: Piia Bartos <piia.bartos.uef.fi<mailto:piia.bartos.uef.fi>>; AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: Re: [AMBER] OPC3-pol
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<mailto: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 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><mailto:piia.bartos.uef.fi<mailto:piia.bartos.uef.fi>>
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Received on Tue Nov 29 2022 - 01:00:02 PST
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