Hi Lukas,
Your files converged for me, though very slowly. I made two changes
1. I changed MDIIS_DEL to 0.3. 0.1 should only be used if you are having trouble converging.
2. I added the version line to the MDL file
%VERSION VERSION_STAMP = V0001.000 DATE = 03/24/22 17:44:15
rism1d won't run without this.
Hope this helps,
TL
Sent with ProtonMail secure email.
------- Original Message -------
On Thursday, March 24th, 2022 at 9:06 AM, Grunewald, Lukas <Lukas.Grunewald.uibk.ac.at> wrote:
> Thanks for your reply!
>
> I calculated the LJ parameters for the dummy atom and created my own mdl-File, but the 1D-RISM calculation is still not converging. Here you can see my created mdl-File and inp-File:
>
> &PARAMETERS
>
> THEORY='DRISM', CLOSURE='KH', !Theory
>
> NR=16384, DR=0.025, !Grid
>
> OUTLIST='uxghctensq', rout=0, !Output
>
> MDIIS_NVEC=20, MDIIS_DEL=0.1, TOLERANCE=1e-12, !MDIIS
>
> KSAVE=-1, maxstep=10000, !Check pointing and iterations
>
> SMEAR=1, ADBCOR=0.5, !Electrostatics
>
> TEMPERATURE=300, DIEPS=78.497, !bulk solvent properties
>
> NSP=1
>
> /
>
> &SPECIES !OPC water
>
> DENSITY=55.296d0,
>
> MODEL="cOPC.mdl"
>
> /
>
> %FLAG TITLE
>
> %FORMAT(20a4)
>
> cOPC
>
> %FLAG POINTERS
>
> %FORMAT(10I8)
>
> 4 3
>
> %FLAG ATMTYP
>
> %FORMAT(10I8)
>
> 1 2 3
>
> %FLAG ATMNAME
>
> %FORMAT(20a4)
>
> O H1 EWP
>
> %FLAG MASS
>
> %FORMAT(5e16.8)
>
> 1.60000000e+01 1.00800000e+00 0.00000000e+00
>
> %FLAG CHG
>
> %FORMAT(5e16.8)
>
> 0.00000000e+00 1.23755293e+01 -2.47510585e+01
>
> %FLAG LJEPSILON
>
> %FORMAT(5e16.8)
>
> 2.12800813e-01 2.12800813e-02 2.12800813e-02
>
> %FLAG LJSIGMA
>
> %FORMAT(5e16.8)
>
> 1.77716726e+00 7.97931377e-01 1.59824682e+00
>
> %FLAG MULTI
>
> %FORMAT(10I8)
>
> 1 2 1
>
> %FLAG COORD
>
> %FORMAT(5e16.8)
>
> 0.00000000e+00 0.00000000e+00 0.00000000e+00 8.72433000e-01 0.00000000e+00
>
> 0.00000000e+00 -2.05146000e-01 8.47971000e-01 0.00000000e+00 9.85730000e-02
>
> 1.25264000e-01 0.00000000e+00
>
> I used the same inp-file for the three point water models and it worked fine. Do you maybe see an error in my mdl-file?
>
> Best regards,
>
> Lukas
>
> ________________________________
>
> Von: tluchko tluchko.protonmail.com
>
> Gesendet: Dienstag, 22. März 2022 18:30:03
>
> An: AMBER Mailing List
>
> Betreff: Re: [AMBER] 1D-RISM with 4-Point water models
>
> Hi Lukas,
>
> I've tried four-point models before but didn't see much benefit. You may have more success.
>
> You do need LJ parameters for the dummy atom and I used the same procedure as for hydrogen atoms in Eqs 21 and 22 of
>
> Luchko T, Gusarov S, Roe DR, Simmerling C, Case DA, Tuszynski J, Kovalenko A (2010) Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber. Journal of Chemical Theory and Computation, 6(3):607–624. https://doi.org/10.1021/ct900460m
>
> Here, oxygen is the enclosing atom and the dummy atom takes the place of hydrogen. You will have to construct your own MDL file.
>
> Hope this helps,
>
> TL
>
> Sent with ProtonMail secure email.
>
> ------- Original Message -------
>
> On Tuesday, March 22nd, 2022 at 3:32 AM, Grunewald, Lukas Lukas.Grunewald.uibk.ac.at wrote:
>
> > Dear Amber Community,
> >
> > I am currently trying to do 1D-RISM and 3D-RISM calculations with 4-Point water models, but I am struggling with defining the right LJ-parameters for the dummy atom for the 1D-RISM calculation.
> >
> > Has anyone of you done 1D-RISM calculations with 4-Point water models before? Did you use LJ-parameters for the 4-Point water model TIP4P on the dummy atom? If so, how did you calculate them? I did not find an input file for a 4-Point water model in the AmberTools and wanted to ask if someone could share his mdl-input file.
> >
> > Thanks for your help,
> >
> > Lukas
> >
> > _______________________________________________
> >
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> >
> > AMBER.ambermd.org
> >
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 24 2022 - 15:30:03 PDT
