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Setup, I/O, and Basic questions
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It would not be very difficult to change the CHARMM source to do this if you are willing to do some coding. A workaround is to write two PDB files, one with the charge in the B-factor column, and one with the radius in the B-factor column; then writ
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Parameter Set Discussion
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I noticed that the NBFIX for SOD and OG2D1 is commented out by default in the file "toppar_water_ions.str" from the latest CHARMM 36 force field parameter set (07/2016 release). Is this because this NBFIX is not recommended or other reasons? Thanks.
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Parameter Set Discussion
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It may be a good idea to do one or two extra species beyond the two you are interested in. You should initially do QM calculations to get the geometries and vibrations and interactions with with water to get the initial charges. Then do crystal cal
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Parameter Set Discussion
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I'm not aware of studies of the dielectric of the TIP3P model as a function of temperature. alex
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Parameter Set Discussion
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I'm not aware of anyone running the Berger force field in CHARMM. However, it should be straight forward to set up the force field in CHARMM. Be sure to use the correct combining rules for the LJ term. alex
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Parameter Set Discussion
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In principle, one could use the PLO2 patch as a model. If you have issues or questions about CHARMM-GUI, there is a specific forum for that, further down on the main forums page.
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Setup, I/O, and Basic questions
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Probably not the best place to start for a new CHARMM user. You may need to contact the author.
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Molecular Dynamics
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Start by reviewing the output log. Did the MINI ABNR process reach 1000 steps, or did it achieve the gradient tolerance and exit before 1000 steps? Does the potential energy appear to be converging over the last 100 steps or so? Also, I believe th
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