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Molecular Dynamics
Jump to new posts Re: Cons fix during MD analysis by EArtikis @ 06/21/18 10:53 AM

Figured it out: scalar move set 0.0 sele segid protein end Immobile atoms are set to 1.0 in IMOVE array.
Parameter Set Discussion
Jump to new posts Re: Parameter File description by Sabya @ 06/21/18 01:11 AM

Thanks a lot!
Setup, I/O, and Basic questions
They are, but most of the people who answer questions here focus on CHARMM usage, and we would need to see what response CHARMM has to a new residue to offer any guidance. I don't use any of the VMD/NAMD ancillary structure tools myself. Also, as n
Position Openings
At the Institute of Molecular Dynamics Simulation of Soft Matter ( at the Technical University of Hamburg the following position - limited until June 30, 2020 for the duration of the project mentioned below - is to be fi
Setup, I/O, and Basic questions
Jump to new posts Re: Steered Molecular Dynamics, regarding by rmv @ 06/18/18 03:27 PM

Questions about scripts from CHARMM-GUI might be best in that forum.
Parameter Set Discussion
The log file is screaming that you have not read all of the the topology and parameter files required for this. At the least, you need to read the ones for nucleic acids before using a stream file that extends those parameters. The stream files usu
Energy terms, Constraints, Restraints, and Solvation
Hi, Thank you for your reply. I tried with the "qmel" tag instead of "elec" in the skip command of my script, yesterday. I believe, "qmel" accounts for both QM and QM/MM electrostatic energy. It seems to be working fine. I have added my latest CHA