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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>
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>
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Received on Thu Mar 24 2022 - 09:30:03 PDT
