Dear Jorden, Thanks for reply. I followed your suggestions and i got an error as follows: Command line: gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr Ignoring obsolete mdp entry 'title'Setting the LD random seed to 1403244422Generated 100032 of the 100128
Hi,
When performing a "make check" on Gromacs 2019.4, I'm getting test 42
failing.
It gives the error:
Mdrun cannot use the requested (or automatic) number of ranks,
retrying with 8
And the mdrun.out and md.log of swap_x reports:
The number of ranks you selected (14) contains a
Hi,
I am currently trying to perform an umbrella simulation on a nucleosome
structure. I am trying to pull the C-terminal tail away from the rest of the
structure.
I am at the pulling stage and run:
gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -r
npt.gro -o
Does the minimization end normally or it crashes?
On Thu, Oct 10, 2019 at 9:27 AM Suprim Tha
wrote:
> I was trying Gromacs based upon the tutorial on
> http://www.mdtutorials.com/gmx/lysozyme/05_EM.html
> However, when I run the command gmx mdrun -v -deffnm em, only em.log,
> em.edr and em.tpr
I was trying Gromacs based upon the tutorial on
http://www.mdtutorials.com/gmx/lysozyme/05_EM.html
However, when I run the command gmx mdrun -v -deffnm em, only em.log,
em.edr and em.tpr are formed but not em. trr and em.gro Without the energy
minimized .gro file, I cannot continue further. Please
Hi Amit,
The metal ion needs to be treated very very carefully so as to maintain
their co-ordination state with the nearby atoms of protein.
To do this, one needs to generate the parameter separately for the complex
formed by the metal ion with the protein residues because due to presence
of metal
Hi
You can check the log file of the cluster output. An average time step will
be given representating the clusters in a tabular format. Note down the
time, accordingly dump it from the trajectory with trjconv. Use an index
file for the protein+ ligand.
Hope it helps.
On Mon, Oct 7, 2019,
