Hi Zhenting,
The meaning of the command line flags can be found in the Amber manual. For the files you have listed
entropy.mol.1.dx
: solvent -T∆S density distribution
potUV.mol.1.dx
: solute-water energy density distribution
solvene.mol.1.dx
: total water energy density distribution
exchem.mol.1.dx
: excess chemical potential energy density distribution
The water-water energy density distribution can be obtained by subtracting potUV from solvene. A convenient Python library for this calculation is
https://github.com/MDAnalysis/GridDataFormats.
Hope this helps,
Tyler
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‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Sunday, October 17th, 2021 at 3:42 AM, Gao Zhenting <zhentgpicasa.gmail.com> wrote:
> Hi there,
>
> I am reading the following paper to learn 3D-RISM
>
> (1)Nguyen, C.; Yamazaki, T.; Kovalenko, A.; Case, D. A.; Gilson, M. K.;
>
> Kurtzman, T.; Luchko, T. A Molecular Reconstruction Approach to Site-Based
>
> 3D-RISM and Comparison to GIST Hydration Thermodynamic Maps in an Enzyme
>
> Active Site. Plos One 2019, 14 (7), e0219473.
>
> https://doi.org/10.1371/journal.pone.0219473.
>
> For the paper, the following command is used to calculated the density and
>
> energy distributions.
>
> $AMBERHOME/bin/rism3d.snglpnt \
>
> - --prmtop fxa-strip.parm7 \
> - --traj fxa-strip.nc --xvv cTIP3P_pse3.xvv \
> - --entropicDecomp --molReconstruct \
> - --guv g \
> - --exchem exchem --entropy entropy --solvene solvene --potUV potUV \
> - --exchemUC exchemUC \
> - --solvcut 999999. --buffer 24. --tolerance 1e-2,1e-6 \
> - --closure kh,pse2,pse3 --uccoeff
>
> 0.0327564,-3.26166,-0.000507492,0.0100166 \
> - --mdiis_restart 100.0 --mdiis_nvec 10\
> - --centering 3 \
> - --verbose 2 > rism.out
>
> There are 4 files which are molecular reconstructed
>
> entropy.mol.1.dx
>
> potUV.mol.1.dx
>
> solvene.mol.1.dx
>
> exchem.mol.1.dx
>
> Which output file is related to "Water-water energy density distributions",
>
> "Solute-water energy density distributions", and "Total water energy
>
> density distributions"?
>
> Best
>
> Zhenting
>
> AMBER mailing list
>
> AMBER.ambermd.org
>
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Oct 18 2021 - 11:00:02 PDT
