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Script Archive
Jump to new posts Generalized Born Energy Calculation by pmj @ Today at 10:45 AM

Hi! I am trying to calculate GBEnr for unperturbed and perturbed systems. I used SCALAR command to change the charge of the atom. However, for different atoms I get the same GBEnr value, so I assume I am missing something in the process. I was tryin
Setup, I/O, and Basic questions
Jump to new posts Re: Does the free charmm version runs in parallel by rmv @ Yesterday at 01:15 PM

We cannot say anything with so little detail. The READ BEFORE POSTING topic found at the top of each forum gives some useful guidelines about how to get help in these forums. Your duplicate post in another forum was deleted, per the guidelines.
Molecular Dynamics
Jump to new posts Equilibrating protein using Drude Model in charmm by Ernesto @ 02/14/19 06:03 PM

Hi, I am having issues equilibration a protein in charmm using the drude model. I ran into the error: ***** In parallel lonepairs must be within group boundary! I am not sure how to rectify this problem and I have been unable to find any related po
Parameter Set Discussion
Hi, I'm trying to generate a CGenFF topology file for a small molecule that contains an aromatic ring with two halogens and I'm having some trouble with the new force field files (which contain lone pairs on the halogens). I have the following ques
Parameter Set Discussion
Jump to new posts Re: SPC/E parameters by lennart @ 02/13/19 05:43 AM

Confirmed typo. Thanks for noting this and reporting it! Alex will replace the Rmin/2 value for SPC/E OT atom with 1.77661. I compared the RDF and diffusion coefficient obtained with the correct value and the current value 1.762827. Positions of pe