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Hi, I am trying to prepare the top and par file for an engineered amino acid in the middle of my protein. I am hoping to obtain the parameter file for this one amino acid from par_all36m_prot.prm and then make some modifications to it. Do I need t
Parameter Set Discussion
Jump to new posts Re: D-peptides in GROMACS by lennart @ Yesterday at 05:34 PM

It is of course always possible to use CHARMM for the simulations...
Energy terms, Constraints, Restraints, and Solvation
Jump to new posts Re: Segmentation fault error setting up a GSBP. by NoviceUser @ 12/06/19 12:52 PM

Thank you very much Josh Buckner. It is working now. Regards, Sridhar
Bug Reports & Fixes
Jump to new posts Re: Patch files by bucknerj @ 12/06/19 07:50 AM

Description This patch fixes compatibility between sccdftb and gsbp. Without this patch, for example, test/clongtest/gsbptest1.inp segfaults. Version Compatibility This patch is for c44b1 and c45a1 Instructions Apply the patch from CHARMM source ro
Setup, I/O, and Basic questions
Jump to new posts Umbrella sampling reaction co-ordinate by vidhya @ 12/06/19 01:59 AM

Hey all, I am using umbrella sampling technique to constraint the distance between two segments of protein defined by the reaction co-ordinate. As per the theory, the distance constraint with a proper force constant should ideally sample around the
Molecular Dynamics
Jump to new posts Re: Question of Pull Efield command by lennart @ 12/03/19 03:58 PM

I agree with Rick. Science is not about asking questions on various internet forums. A good way to learn is to perform small experiments in order to either narrow down a problem or to understand how something actually works. For instance regarding th
Script Archive
Jump to new posts Re: applying crystal symmetry by rmv @ 12/02/19 04:45 PM

Yes, for the unit cell only the lattice constants are needed, so it is translation only (P1).