Geometric flow test suite for APBS

[sobolevnrm]

@lizutah

[keith923]

There is currently a single geoflow test case, located at ./examples/geoflow. Below is the contents of the .in file.

read
    mol pqr imidazole_zap.pqr        
end
elec name comp_solv        # Solvated complex
    geoflow-auto

    lpbe
    bcfl mdh
    mol 1

    grid 0.23 0.25 0.27     # grid spacing                      (dcel)
    pdie 1.5                # Solute dielectric                 (epsilon_p)
    sdie 80.00              # Solvent dielectric                (epsilon_s)
    press 0.008             # pressure kcal/(mol*A^3)           (pres)
    gamma 0.0001            # surface tension kcal/(mol*A^2)    (gama)
    bconc 0.03346           # bulk solvent density A^-3         (density)
    vdwdisp 0               # van der wal dispersion (on/off)   (vdwdispersion)
end

quit

[astevens-pnnl]

The parameter names in the third column correspond to the names in the geoflow code.
There are also other test cases in the geoflow folder but they are not apbs test cases (and not pqr files). For the all of the cases we can supply a forcefield (or not, the case below), which is not currently retrieved by the parser and not passed into geoflow.

From: keith923 <notifications@github.commailto:notifications@github.com>
Reply-To: Electrostatics/apbs-pdb2pqr <reply@reply.github.commailto:reply@reply.github.com>
Date: Friday, 4 April 2014 1438
To: Electrostatics/apbs-pdb2pqr <apbs-pdb2pqr@noreply.github.commailto:apbs-pdb2pqr@noreply.github.com>
Subject: Re: [apbs-pdb2pqr] Geometric flow test suite for APBS (#29)

There is currently a single geoflow test case, located at ./examples/geoflow. Below is the contents of the .in file.

read
mol pqr imidazole_zap.pqr
end
elec name comp_solv # Solvated complex
geoflow-auto

lpbe
bcfl mdh
mol 1

grid 0.23 0.25 0.27     # grid spacing                      (dcel)
pdie 1.5                # Solute dielectric                 (epsilon_p)
sdie 80.00              # Solvent dielectric                (epsilon_s)
press 0.008             # pressure kcal/(mol*A^3)           (pres)
gamma 0.0001            # surface tension kcal/(mol*A^2)    (gama)
bconc 0.03346           # bulk solvent density A^-3         (density)
vdwdisp 0               # van der wal dispersion (on/off)   (vdwdispersion)

end

quit

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/29#issuecomment-39597155.

[keith923]

There are only three files in the geoflow folder. Two .pqr files and one .in file. If other tests exist, it may be nice to locate them.

[astevens-pnnl]

Not the test/example folder, the src folder.

From: keith923 <notifications@github.commailto:notifications@github.com>
Reply-To: Electrostatics/apbs-pdb2pqr <reply@reply.github.commailto:reply@reply.github.com>
Date: Friday, 4 April 2014 1849
To: Electrostatics/apbs-pdb2pqr <apbs-pdb2pqr@noreply.github.commailto:apbs-pdb2pqr@noreply.github.com>
Cc: Andrew Stevens <andrew.stevens@pnnl.govmailto:andrew.stevens@pnnl.gov>
Subject: Re: [apbs-pdb2pqr] Geometric flow test suite for APBS (#29)

There are only three files in the geoflow folder. Two .pqr files and one .in file. If other tests exist, it may be nice to locate them.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/29#issuecomment-39619148.

[lizutah]

duplicate of #224

[lizutah]

from #224, needs to include small molecules and 1a1p

[sozenoid]

Hello,
I think there is still ambiguity in APBS 3.0.0 (that does not output energy units in the geoflow computation) and the definition of the keywords on the website. Are gamma and press given in kcal or kJ? Thank you very much for writing this code. I'm very grateful for it.

[sobolevnrm]

@sozenoid - thank you for the feedback. I've created a new issue #606 that focuses on this problem.