Re: [AMBER] OPC3-pol

From: Piia Bartos via AMBER <amber.ambermd.org> Date: Sat, 26 Nov 2022 08:06:19 +0000

--
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>
________________________________
From: Saeed Izadi <izadi.vt.edu>
Sent: Thursday, November 24, 2022 09:08
To: Piia Bartos <piia.bartos.uef.fi>; AMBER Mailing List <amber.ambermd.org>
Cc: Carlos Simmerling <carlos.simmerling.gmail.com>
Subject: Re: [AMBER] OPC3-pol
I wonder if there is an issue in your post-processing and visualization of the trajectory than with the simulation itself. Did you process your trajectory in cpptraj (e.g. "autoimage" and "rms first")  before visualization? If so, would you share your cpptraj scripts as well?
On Tue, Nov 22, 2022 at 11:58 PM Piia Bartos via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
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 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><mailto: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><mailto: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 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><mailto:piia.bartos.uef.fi<mailto:piia.bartos.uef.fi>><mailto:piia.bartos.uef.fi<mailto:piia.bartos.uef.fi><mailto:piia.bartos.uef.fi<mailto:piia.bartos.uef.fi>>>
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