How can I make GROMACS use devtoolset-6?
[shlomit@cn gromacs-2019.5]$ type gcc
gcc is /bin/gcc
[shlomit@cn gromacs-2019.5]$ scl enable devtoolset-6 bash
[shlomit@cn gromacs-2019.5]$ type gcc
gcc is /bin/gcc
Shlomit
On 15/01/2020, 12:07,
The simulated tempering options haven't been as well tested as the
hamiltonian expanded ensemble version. The weights SHOULD be showing up in
the column that says -nan, but clearly they aren't. If you file a redmine
issue, I may be able to take a look, but it might take a while to address.
On
Hello,
I am interested in using simulated tempering in GROMACS (2019.5) under the
expanded ensemble options. Is there a way to monitor the ensemble weights
as the simulation progresses? I think in theory they are supposed to be
printed out in the log file, but it is only printing 0, -nan, and
Dear Dr. Justin Lemkul,
Can you explain why the D-H-A is 150?
If H-D-A is 30, then D-H-A should be smaller than 150 degrees.
Since the sum of interior angles of a triangle should be 180 degrees...
See the following triangle.
H
D
On 1/15/20 6:58 PM, ZHANG Cheng wrote:
Hi Justin, what kind of information should I look at in the log files? They are too big
to paste here. Would it be possible if you can see them
athttps://github.com/lanselibai/gromacs-20200115;?
It doesn't look like either of those runs actually
Hi Justin, what kind of information should I look at in the log files? They are
too big to paste here. Would it be possible if you can see them
athttps://github.com/lanselibai/gromacs-20200115;?
Thank you!
--Original--
From:"ZHANG Cheng"<272
On 1/15/20 2:38 PM, Marcelo Depólo wrote:
Hi everyone!
I was wondering about the cmaptypes format within cmap.itp file.
[ cmaptypes ]
C N CT C N 1 24 24\
I understand that C-N-CT-C = phi, N-CT-C-N = psi and 24x24 is the grid
size. What does this '1' mean?
Probably a useless/dummy function
On 1/15/20 2:38 PM, ZHANG Cheng wrote:
I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the
preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro"
and "-r npt.gro" are
Hi everyone!
I was wondering about the cmaptypes format within cmap.itp file.
[ cmaptypes ]
C N CT C N 1 24 24\
I understand that C-N-CT-C = phi, N-CT-C-N = psi and 24x24 is the grid
size. What does this '1' mean?
Thanks in advance!
--
Marcelo Depólo Polêto
Postdoctoral Researcher
BIOAGRO -
I have a nearly identical run using the "VERSION 2019.3" compared to my
previous "VERSION 5.1.1". Everything during the preparation is the same except
"-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro"
and "-r npt.gro" are added in the grompp commands for NVT, NPT and
Dear all,
I am aware of the "gmx genconf -f time.gro -nbox 2 2 2 -o 2times.gro" in
order to expand a gro file 2 times in all directions. I wonder if it is
possible to expand a xtc trajectory and outpout a larger trajectory in the
same way?
According to genconf man page I see that the input could
On 1/15/20 11:57 AM, Pandya, Akash wrote:
Hi all,
I wanted to ask a couple of questions about the hydrogen bonding calculation
in Gromacs.
1. Why is the default angle cutoff 30 degrees? The reason I ask this is
because I’ve seen in other packages with higher angle cutoffs.
It
On 1/15/20 6:32 AM, gmx user1 wrote:
Dear GMX users
I am doing umbrella sampling to obtain a PMF relative to the translocation
of a ligand within a membrane protein.
I want to add an harmonic potential to restrain the center of mass of the
ligand in each window ,
similarly to the protocols
On 1/15/20 12:27 AM, Sundari wrote:
I tried all the options.. I load gro file instead of xtc. At zero frame I
gave representations new cartoon + secondary structure.. then I calculate
sec str details by going on vmd timeline.
I don't know what I am missing.. I am doing the same which I used
Hydrogen bonding is approximated by charge-dipole interaction, which is
very orientation-sensitive, the energy of this kind interactions
are proportional to the cosine of the angle.
https://en.wikibooks.org/wiki/Molecular_Simulation/Charge-Dipole_Interactions
On Wed, Jan 15, 2020 at 5:59 PM
Hi all,
I wanted to ask a couple of questions about the hydrogen bonding calculation
in Gromacs.
1. Why is the default angle cutoff 30 degrees? The reason I ask this is
because I’ve seen in other packages with higher angle cutoffs.
2. What’s the best way to define cutoffs for my
Dear GMX users
I am doing umbrella sampling to obtain a PMF relative to the translocation
of a ligand within a membrane protein.
I want to add an harmonic potential to restrain the center of mass of the
ligand in each window ,
similarly to the protocols used by Subramanian et al (
Dear Gromacs users
I am facing this error during free energy calculation of protein-ligand for
which I have applied restrained to some atoms of protein residue and
ligand.
A list of missing interactions:
Restraint Pot. of 1 missing 1
Molecule type 'Protein'
the first 10 missing
Dear all,
I have calculated the c-alpha RMSD of dimer having 7 residues peptide each
by using command gmx rms. But the calculated RMSD 14 Angstorm is very high,
although I have applied all pbc conditions. Anybody can suggest me why so
much high RMSD is coming or is it possible.
--
Ashma Khan
On Wed, 15 Jan 2020 at 11:07, Tru Huynh wrote:
>
> gcc is /opt/rh/devtoolset-6/root/usr/bin/gcc
>
Good, so is Cmake using it? (e.g. remove the build dir and run cmake again
to see what it first reports, or inspect $builddir/CMakeCache.txt for the
compiler setting)
Mark
--
Gromacs Users
On Wed, Jan 15, 2020 at 08:50:46AM +, Shlomit Afgin wrote:
>
> Hi,
> I tried to install GROMACS 2019.5 on CentOS7,
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>
> I have already installed devtoolset-6 and still get this error:
installed, but not using it?
I ran:
cat /proc/cpuinfo | grep -i avx512
and got:
avx512f avx512dq avx512cd avx512bw avx512vl
So I thought I can use it. Am I wrong?
Shlomit
On 15/01/2020, 11:14, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Szilárd Páll" wrote:
Hi,
What
Are you actually using the GCC from the devtoolset or the default one? Cmake
tells you at the very beginning which compiler it is using.
Roland
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se users-boun...@maillist.sys.kth.se> On Behalf Of Shlomit Afgin
>
This is very helpful thank you. I think I can use this. I will also ask the
vmd mail list.
Best, Miro
Le mer. 15 janv. 2020 à 19:35, Alessandra Villa <
alessandra.villa.bio...@gmail.com> a écrit :
> Hi,
> One of the criteria that VMD uses to define bond is distance criteria. When
> you source
Hi,
What hardware are you targeting? Unless you need AVX512 support, you could
just manually specify the appropriate setting in GMX_SIMD, e.g.
-DGMX_SIMD=AVX2_256 would be appropriate for most cases where AVX512 is not
supported.
Cheers,
--
Szilárd
On Wed, Jan 15, 2020 at 9:51 AM Shlomit Afgin
Hi,
I tried to install GROMACS 2019.5 on CentOS7,
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
I have already installed devtoolset-6 and still get this error:
-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
Hi,
One of the criteria that VMD uses to define bond is distance criteria. When
you source your gro file, this criteria is applied.
One way one, I have used is to not visualize undesired bonds, is the
following:
delete the undesired bonds, save the vmd setting (*.vmd file), load the
setting
27 matches
Mail list logo
