Gmx editconf you can use with -translate flag...after that merz the
coordinates of two water droplets. I hope this may help you.
On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, <
devargyachakraborty@gmail.com> wrote:
> I have an equilibrated droplet of water. What I want to do is
I have an equilibrated droplet of water. What I want to do is replicate
that droplet in the x direction. So that my simulation box will carry two
water droplets. Is that possible in gromacs. If yes please guide me.
Thank you
Devargya Chakraborty
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Dear GMX users,
I would like to perform MD simulations of solutions applying electric
fields such as the microwave heating process. Is it possible to perform in
gromacs?
1. How can I set the external electric field in the simulations?
(from the user guide, I understood that I need to set 4
Hi,
Depends when you see them. From mdrun, you're generally blowing up (see
user guide and FAQ list). From tools, maybe your input data is somehow bad
(or bad in part, so try different parts), or you ran into a silent size
limitation in the code (see if a smaller data set works and if so file a
Den 2020-03-09 kl. 20:14, skrev Travis Meyer:
Hello all,
I am a very new user to GROMACS and MD simulations in general. While going
through some tutorials and other test simulations I've been getting some
floating point exception errors. I recognize that there are a vast number of
problems
Hello all,
I am a very new user to GROMACS and MD simulations in general. While going
through some tutorials and other test simulations I've been getting some
floating point exception errors. I recognize that there are a vast number of
problems that could be causing this - I am not looking for
On 3/9/20 7:10 AM, Adarsh V. K. wrote:
Dear all,
How to solve this error ?
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1
The command returns following errors while suing ions.mdp
-
NOTE 1 [file ions.mdp]
ERROR 1
On 3/7/20 2:10 PM, Eduardo Mayo wrote:
Hi!,
I mean the page
http://www.gromacs.org/Downloads/User_contributions/Force_fields
has
a amber14sb.ff.tar.gz amber14sb_OL15.ff_corrected-Na-cation-params.tar.gz
but at the top of the page it is a warning that say "These force fields are
provided
In most cases this means that the exact same line is given more than once. I
would start from there.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Adarsh V. K.
Sent: Monday, March 9, 2020 1:26 PM
To:
Hi Andreas,
Sorry for the delay.
I can confirm the regression. This affects the energy calculation steps
where the GPU bonded computational did get significantly slower (as a
side-effect of optimizations that mainly targeted the force-only kernels).
Can you please file an issue on
Dear Gromacs,
There seems to be very little explanation on the "-surface" and "-output"
options of "gmx sasa":
-surface: This should always consist of all non-solvent atoms in the system.
The area of this group is always calculated
-output: can specify additional selections, which should be
Hi,
The code is tested extensively on a range of compilers, so we believe it is
correct and compliant. In particular, you're using gcc 6.1.0 and GROMACS
tests with 6.4.0, so the issue might have been fixed in the meantime. As
newer versions of gcc and cuda will give better performance, I suggest
Hi,
Check out the GROMACS FAQs - this question is a very frequent one! :-)
Mark
On Mon, 9 Mar 2020 at 11:42, Sadaf Rani wrote:
> Dear Gromacs users
>
> I am running a free energy test calculation and using position restraints
> for all of the system. At the end of pressure equilibration I am
Dear Gromacs users
I am running a free energy test calculation and using position restraints
for all of the system. At the end of pressure equilibration I am
getting negative average pressure as below:-
Energy Average Err.Est. RMSD Tot-Drift
Hi all
After attempting to install GROMACS 2020 on new system, I get the error below.
The system details & other details are below the error.
cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_INSTALL_PREFIX=/home/b5018993/src/gromacs-2020
-DCMAKE_C_COMPILER=gcc
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