Hi
What error you are getting?
On Fri 20 Dec, 2019, 1:14 PM Devargya Chakraborty, <
devargyachakraborty@gmail.com> wrote:
> -- Forwarded message -
> From: Devargya Chakraborty
> Date: Thu, 19 Dec 2019 at 18:17
> Subject: setting ionic liquid simulation in gromacs
> To:
>
On 12/20/19 6:07 AM, Suvardhan Jonnalagadda wrote:
Hi,
Thanks for the reply.
I have included it and rerun my system. Still problem prevails.
energrps are not required for LJ 1-4 energies, as these are
intramolecular and energygrps correspond strictly to intermolecular
interaction energies.
Hi GROMACS users,
The GROMACS 2020 release candidate is now out and available!
As before, we are making the testing versions available for you to be
able to get feedback
on how well things are working, and what could be improved or if there
are any bugs
in the code we have missed ourselves.
Dear gmx-users,
I am looking for the explicit formula of the wall potentials implemented when
one uses the wall mdp options.
In the gromacs user-guide, there are indications on the dependence relative to
the distance z to the wall : for example LJ 9-3,
I understand it is a sum of a contribut
Dear Gromacs users
I want to run free energy calculation of a protein-ligand complex by
putting distance, angle and dihedral restraints between ligand and protein.
Before that, I run 1ns MD (without free energy input) in order to know that
my ligand restraints are working well or otherwise. However
Hi,
I am facing the same issue in version 5.1.4 as well.
I have 1-4 interactions in my system (mentioned 'gen-pair' yes in
'forcefield.itp file)
Is there a way to extract the 1-4 interaction energy?
Thank you
On Fri, Dec 20, 2019 at 2:43 PM Mark Abraham
wrote:
> Hi,
>
> On Thu., 19 Dec. 2019,
The problem has been solved by installing ocl-icd-opencl-dev. I think this package should be mentioned in the installation guide. 19.12.2019, 01:20, "Mark Abraham" :Hi,If you use -DOpenCL_LIBRARY then it has to indicate the location oflibOpenCL.so because you've short-circuited any attempt to find
Hi,
The fftw build you are trying to do uses gcc by default, and your gcc is so
old that AVX512 didn't exist yet, so it cant compile for it. Since you're
using the Intel compiler, it's easiest to also use its fft library with
cmake -DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=mkl
Harder is to updat
Hi,
On Fri., 20 Dec. 2019, 09:59 Sina Omrani, wrote:
> Hi,
> I have a problem when I use CO2 model with virtual sites during energy
> minimization. I used itp file in the md tutorial and beside the fact that
> some of my water molecules can not be settled, I get a positive potential
> energy and
Hi,
On Thu., 19 Dec. 2019, 18:41 Suvardhan Jonnalagadda,
wrote:
> Hi All,
>
> *"GROMACS: VERSION 4.5.5; Precision: single"*
>
This software is nearly a decade old and is no longer supported. Please
update.
I have performed an md simulation for 1 time step, on a single molecule
> with 17 atoms.
Hi,
I have a problem when I use CO2 model with virtual sites during energy
minimization. I used itp file in the md tutorial and beside the fact that some
of my water molecules can not be settled, I get a positive potential energy and
high force on molecules. Is something wrong?
And another quest
Hi,
Maybe the nvt.log file provides you more information on the problem
Best regards
Alessandra
On Fri, Dec 20, 2019 at 9:40 AM Bratin Kumar Das <
177cy500.bra...@nitk.edu.in> wrote:
> Dear all,
> During running nvt equilibration I got the following error.
> gmx mdrun -v -s nvt.tp
Hi
On Thu, Dec 19, 2019 at 3:41 PM Maria Luisa wrote:
> Dear users,
> I want to constraints a group of molecules inside a tri-layer structure.
> How can I label and fix these molecules ?
>
>
Depends on the problems, but to fix atoms to a reference position, you can
use position restraints
(
http
Dear all,
During running nvt equilibration I got the following error.
gmx mdrun -v -s nvt.tpr -deffnm nvt -cpi nvt.cpt -append
:-) GROMACS - gmx mdrun, 2016.5 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C
14 matches
Mail list logo