Dear Gromacs Users,
I am trying to obtain an average structure in addition to the rmsf from my
trajectories.
I tried doing that using 'gmx rmsf', but I was not successful yet.
Thanks in advance for all suggestions!
Best,
Jacek
Dr. Jacek Kozuch
Hi all,
I've seen that recent tip7p water model
(https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03149) and wanted to try it out.
However, I couldn't find or I missed where the itp and gro files are deposited.
Anybody knows where to find them?
Thanks a lot in advance!
Best,
Jacek
[https://pubs.ac
Dear all,
I've seen the recent publication about the tip7p model
(https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03149) and wanted to try it
out in some simple MD simulations.
Since I am still a pretty new Gromacs user, I didn't want to build the itp
file myself and, potentially or most probably, me
Hi all,
I am currently trying out various water models for some solute/solvent
systems and I was wondering if there are any (reliable) anharmonic/Morse
flexbile water models that can be used in Gromacs?
I've seen that can set [ Morse ] for bonds, but don't want to start doing
random changes to av
Hi,
Does anybody know how to define for a specific bond a double-well potential?
I've looking into the definitions in the gromacs manual
(manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html
and
manual.gromacs.org/current/reference-manual/functions/bonded-interactions
Dear all,
I am a bit confused about [ dihedral constraints ].
I was planning to contraint a dihedral in a "flat-bottom" way, so that
e.g. angles between 120 and 240 deg are sampled, but above 240 and below
140 are basically "not allowed". In other words, I just want a harmonic
potential, where th