Hi
Give here the full error
On Thu 13 Jun, 2019, 1:35 AM Mark Abraham, wrote:
> Hi,
>
> Was grompp exiting normally, or crashing? Are you looking in the right
> place, for a file of the right name? :-)
>
> Mark
>
> On Wed., 12 Jun. 2019, 18:42 Israel Estrada, wrote:
>
> > Hello users,
> >
>
Hi Mahsa,
Thanks very much for your feedback. Those look like useful changes to the
code. Can you please open an issue at https://redmine.gromacs.org with that
information? You'll also be able to attach files, unlike on this list :-)
Mark
On Wed., 12 Jun. 2019, 15:21 Mahsa, wrote:
> Hi again,
Hi,
On Wed., 12 Jun. 2019, 07:47 Prasanth G, Research Scholar, <
prasanthgha...@sssihl.edu.in> wrote:
> Dear Bratin,
>
> Thank you for your prompt response. would using an isotropic pcoupletype
> have any effect on a membrane protein simulation?
>
It will keep the box vectors in the same ratio,
Hi,
Was grompp exiting normally, or crashing? Are you looking in the right
place, for a file of the right name? :-)
Mark
On Wed., 12 Jun. 2019, 18:42 Israel Estrada, wrote:
> Hello users,
>
>
> I'm running into problems trying to grompp; I'm using the command
>
>
> gmx grompp -f ions.mdp -c
Hi,
The most likely explanation here is that the starting configuration isn't
very happy (box of wrong size? equilibrating with the unsuitable
parrinello-rahman algorithm?). The CPU-only run does a different domain
decomposition than the run with GPUs, leading to a different relaxation
Hello
I fudged a restart on gromacs 2018 and am missing 195 femtoseconds from my
trajectory. This shouldn't matter because I only need a 10 picosecond
resolution trajectory. However, when I try to correct the timestep with
trjconv and -timestep it doesnt seem to have done anything.
*gmx trjconv
Hi,
I've been running into following issue in my MD simulation:
While running the simulation on CPUs everything worked fine. But when running
the simulation with the same input files on GPUs only minimization and NVT
equilibration run successfully. When starting the NPT equilibration the system
Hello,
I have a 200ns trajectory of protein-water-urea mixture, saved at 2ps
interval. I want to calculate the angle distribution of water molecule
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Hello,
I am trying to start a minimization in gromacs with a system containing a
LC and a IL, and when I try to introduce water in the system and minimize,
while running grompp:
gmx grompp -f em.mdp -c system-solvated.gro -p system-solvated.top -o
system-solvated-em.tpr
*And the
Hello users,
I'm running into problems trying to grompp; I'm using the command
gmx grompp -f ions.mdp -c etc_box.gro -o ions.tpr -p topol.top
and the process shows no error messages, but output files are not being
generated. I'm running this on a small molecule, about 20 atoms, with the
Hi again,
Something went wrong with the equations which I tried to show.
So for the first equation please see eq. 9 in this paper:
https://aip.scitation.org/doi/10.1063/1.2868752
and the second missing formula is:
1 / 6*V*K_B*T = 7.20677e-12
Best regards,
Mahsa
On Wed, Jun 12, 2019 at 3:12
Hi gmx-users,
I use gmx current tool to calculate static conductivity by version 2018:
gmx current -f md.xtc -o -dsp -md -mj -temp 423 -nojump -n index.ndx -s
topol.tpr
Indeed the tool is useful, but I think some parts in the output are
confusing and need to be improved.
I think the generated
Hello,
I have a 200ns trajectory of protein-water-urea mixture, saved at 2ps
interval. I want to calculate the angle distribution of water molecule
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*
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