Dear Gromacs Users,
My system contains two micelles. In order to calculate the radius of gyration
for two micelles, I need to select molecules in each micelle. Is there any tool
available in Gromacs to do that? If available, what options in the -h should I
use to get the information I want.
Than
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
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 (
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
e
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 mdr
With gmx_mpi mdrun -v -deffnm nvt_pr, there is not error.
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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:
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
this