[gmx-users] Simulating crystal structures

Hello, is GROMACS able to simulate crystaline structures properly? I have two residues parametrized that build up the crystal structure. The unit cell is however cut off at the edges (periodicity). So the question is if i enable periodic boundry conditions will GROMACS be able to handle the

Re: [gmx-users] topology for bilayer graphene oxide

The most useful method in terms of understanding both Gromacs and graphene oxide (GO) would be to follow the existing tutorials for pristine graphene/CNTs and then extending the approach to GO. That said, it is very strange that all these topology servers fail on things as structurally simple

[gmx-users] topogen usage

Dear Users, Although topogen is a bit dated it seems to work well for ‘smaller’ polymers -500 atoms- and builds a single file itp. However in making a file for nylon 12 1000 atoms , a ‘central’ itp was create and separate files were made for section_dihedrals, section_bonds etc. Are these to

[gmx-users] topology for bilayer graphene oxide

Hi Users How do I generate the required .itp file to perform MD simulation for bilayer Graphene oxide. structure in OPLSAA ff? Adapting the already available server or script to generate the itp file look little vague. Andre Minoia is pretty easy for monolayer sheets or CNTs. In case of this

Re: [gmx-users] Inconsistency in user input:

Hi, Things like multiple energy groups have never been supported on GPUs. Old versions of GROMACS ran them anyway, filling most energy groups values with zeros, if I recall correctly. However, that behaviour is somewhere between rather surprising and wrong (since you specified -nb gpu), so now

[gmx-users] Inconsistency in user input:

Dear gromacs users, I am doing md simulation (nvt equilibration step) using gromacs version 2018.2. After using (gmx_mpi mdrun -v -deffnm nvt_pr -nb gpu), I encountered with: Program: gmx mdrun, version 2018.2 Source file: src/gromacs/taskassignment/decidegpuusage.cpp (line 292) Function:

[gmx-users] Inconsistency in user input:

With gmx_mpi mdrun -v -deffnm nvt_pr, there is not error. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit