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    LSchwiebert
    @LSchwiebert
    Thanks for setting this up. I think this is a better way to organize our conversations than through email.
    Younes Nejahi
    @YounesN
    Of course.
    I agree. Faster and easier way to communicate for everyone including us and anyone else who uses our code.
    Mohammad Soroush Barhaghi
    @msoroush
    I think we need to make some rooms for Issue, Suggestion.
    LSchwiebert
    @LSchwiebert
    @msoroush This is a good idea. Anything that helps organize the communication and makes it easy to find threads later.
    Younes Nejahi
    @YounesN
    Just created them. Please let me know if you are not able to see them.
    Dr. Anand Bharti
    @gandhiforbes
    Thanks Prof. Jeffrey Potoff and Prof. Loren Schwiebert for developing GOMC. Earlier I used Towhee for performing monte carlo simulation. Now I am switching to GOMC for VLE study.
    I have one query: I am planning to use TraPPE/OPLS force field parameters. But I couldn't figure out how to use TraPPE/OPLS force field parameters in CHARMM format parameter file especially dihedral parameters?
    Dr. Anand Bharti
    @gandhiforbes

    Unable to run this file:

    psfgen<<ENDMOL

    topology ./top_NobleGases.inp

    exec grep "AR" packed_argon_krypton_liq.pdb > Ar.pdb
    exec grep "KR" packed_argon_krypton_liq.pdb > kr.pdb

    segment AR {
    pdb ./Ar.pdb
    first none
    last none
    }

    segment KR {
    pdb ./Kr.pdb
    first none
    last none
    }

    coordpdb ./Ar.pdb AR
    coordpdb ./Kr.pdb KR

    writepsf ./START_BOX_0.psf
    writepdb ./START_BOX_0.pdb

    file delete Ar.pdb

    file delete Kr.pdb

    Jeffrey Potoff
    @jpotoff
    @gandhiforbes The conversion from the old OPLS style to CHARMM style dihedral potential is straightforward. By changing the phase angle, one can change the sign before the cosine term. For example, the torsion for the TraPPE alkane force field looks like this in "CHARMM format".
    !atom types Kchi n delta description
    X CH2 CH2 X 0.00 0 0.0 ! TraPPE I (ex. n-butane)
    X CH2 CH2 X 355.0 1 0.0 ! ""
    X CH2 CH2 X -68.19 2 180.0 ! ""
    X CH2 CH2 X 791.32 3 0.0 ! ""
    In OPLS format, you would have 355(1+cos(x))-68.19(1-cos(2x))+781.32(1+cos(3*x))
    In "CHARMM format", this becomes: 355(1+cos(x+0))-68.19(1+cos(2x+180))+791.32(1+cos(3*x+0))
    It's always helpful to put these in a spreadsheet to check that the two functional forms are producing the same dihedral potential.
    Jeffrey Potoff
    @jpotoff
    @gandhiforbes Regarding the "unable to run issue", for that script to work, you must have VMD (https://www.ks.uiuc.edu/Research/vmd/) installed.
    @gandhiforbes Also, we have example parameters for the TraPPE force field available here: https://github.com/GOMC-WSU/Forcefields/tree/master/TraPPE, you can follow that style and create a similar parameter file, but with OPLS parameters. If you tell use the compounds you are interested in running, we can help you create an OPLS parameter file that will work with GOMC.
    Dr. Anand Bharti
    @gandhiforbes
    Thanks a lot Prof. jpotoff for useful suggestions. I will try to implement the given suggestion. I will come back to you if I face any problem.
    Mohammad Soroush Barhaghi
    @msoroush
    @gandhiforbes if you are using OPLS, you also need to set VDWGeometricSigma true for combining rules in OPLS forcefield. @jpotoff already explained the dihedral parameters, but I want to add that in GOMC we support Charmm and Mie style parameter files. For more details regarding the difference between these two styles, you can refer to manual.
    In summary, Charmm unit is in kcal/mol and you don't need to define the repulsion exponent, here is an example
    Mie units is in K and you must define the repulsion exponent, here is an example
    Dr. Anand Bharti
    @gandhiforbes
    Thanks @msoroush for the suggestions. I will go through the mentioned examples.