or which there were apparently no static
> equivalents.
>
> Mark
>
> On Sun, Jul 22, 2018, 18:16 Shayna Hilburg wrote:
>
> > Hi all,
> >
> > I'm trying to install GROMACS 2018 for use on GPUs. We typically keep the
> > software on the master node and j
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
-DCMAKE_INSTALL_PREFIX=/mnt/shared/gromacs2018 -DGMX_BUILD_SHARED_EXE=OFF
-DGMX_FFT_LIBRARY=fftw3 -DCUDA_TOOLKIT_ROOT_DIR=/mnt/shared/cuda8*
Thank you!
Shayna
--
Shayna Hilburg
Doctoral Candidate
Massachusetts Institute of Techn
That error is solved by switching to *pull_coord1_geometry =
direction-periodic* to let it move over periodic boundary conditions as
described here: http://manual.gromacs.org/online/mdp_opt.html#pull
On Sat, Jun 30, 2018 at 12:07 AM Chenlin Lu wrote:
> Hello,
>
>
> I am doing umbrella sampling
Hey all,
The "gmx wham" command literature says that it is not intended for multiple
coordinates but might work. Does anyone have more elaboration on how the
algorithm works to combine coordinates and/or if there is a way to separate
it and analyze them 1 by 1?
Thanks!
-Shayna
--
Gromacs Users m
Hi,
I have a a couple of SPC/E water molecules restrained within a low
dielectric medium in a system that also contains ions (restrained to a
different region of the box). I was able to run the simulation for several
nanoseconds before it crashed due to "water molecule ... can not be
settled". The
Hi all,
I'm setting up a system and I am getting a non-zero total charge of
approximately 0.0002. I have several thousand ions in a system where the
cation is a single atom of charge +2, and then the anion is a CO3 molecule
(C with +1.3 and O with -1.1). If I change the partial charges to be full
