[gmx-users] Average structure from trajectory

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

[gmx-users] Anharmonic/Morse flexible water

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

[gmx-users] Dihedral Restraints

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

[gmx-users] Double-well potential for bonded interaction

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

[gmx-users] itp file for TIP7P

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,

[gmx-users] GROMACS - tip7p itp and gro files - couldn't find them anywhere

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