Hello Piia,
Just want to follow up on this -- were you able to run your simulations
with OPC3-pol after the last email?
We added a pre-equilibrated waterbox for OPC3-pol -- `OPC3POLBOX` to AMBER
23, now you can do `solvatebox molc OPC3POLBOX 10.0` in tLEAP instead of
`O3P` as in the previous version. More details can be found in Amber23
manual.
Best regards,
Yeyue
On Tue, Nov 29, 2022 at 9:50 AM Yeyue Xiong <xiongyy.vt.edu> wrote:
> Hi Piia,
>
> Could you try replacing this line `solvatebox molc OPC3BOX 10.0` with -
> `solvatebox molc O3P 10.0` ? (this might need a longer equilibration stage
> since it's not a pre-equilibrated water box like `OPC3BOX` etc.)
>
> It looks like tleap solvated the system with opc3(OP3) while still
> thinking the WAT is opc3-pol (O3P).
>
> Best,
> Yeyue
>
> On Sat, Nov 26, 2022 at 12:06 AM Piia Bartos via AMBER <amber.ambermd.org>
> wrote:
>
>> Hi,
>>
>> I can share the cpptraj as well. Like the other scripts, this works fine
>> with the other water models, so my assumption is that there is some bug...
>>
>> Here is the script:
>> parm structure_HMR.prmtop
>> reference structure.inpcrd [ref]
>> trajin prod1.nc 1 last 1
>>
>> #strip :WAT outprefix stripped
>> center .CA mass origin
>> image origin center familiar
>> rms ref [ref] mass out rmsd.out .CA fit
>> trajout stripped.xtc
>>
>> 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>
>>
>> ________________________________
>> 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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Received on Fri May 19 2023 - 18:00:03 PDT
