On 1/6/20 9:40 PM, 변진영 wrote:
Dear everyone, Happy New year!
I have gone through the Justin Lemku tutorial for Umbrella Sampling. During
tutorial, When I treid to input the command line:
gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r
npt0.gro -n index.ndx -o
Dear everyone, Happy New year!
I have gone through the Justin Lemku tutorial for Umbrella Sampling. During
tutorial, When I treid to input the command line:
gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r
npt0.gro -n index.ndx -o umbrella0.tpr
I have met two warnings and
On 1/6/20 4:46 PM, Marcelo Depólo wrote:
Hi everybody! Happy new year! =)
I would like to understand a little bit better the CMAP format of
charmm27.ff within GROMACS. I've looked up in the manual but found little
information.
I understand that it is defined by 5 atoms (1-4 phi and 2-5
On 1/6/20 2:59 PM, Christos Deligkaris wrote:
Justin, thank you.
I have implemented the pull code but that also exhibits the same error when
I use 12 cores (failed at about 2ns) and the simulation goes on fine when I
use 6 cores (now at about 32 ns).
I tried using the v-rescale thermostat
On 1/4/20 1:17 PM, Quin K wrote:
Dear Proffesor Lemkul,
I have given below the MD RMSD for complex, and noted that Ligand is
getting detached again. When I viewed the trajectory on VMD it was
confirmed. The ligand did not abruptly got dislodged instead it slowly
came out of binding pocket
Hi,
As a work-around it is possible to put "#pragma intel optimization_level 2" in
front pull_calc_coms in file src/gromacs/pulling/pullutil.cpp or use Intel
compiler 2019u4 which doesn't have the problem.
Lowering the optimization for the one function shouldn't have a significant
impact on
Hi everybody! Happy new year! =)
I would like to understand a little bit better the CMAP format of
charmm27.ff within GROMACS. I've looked up in the manual but found little
information.
I understand that it is defined by 5 atoms (1-4 phi and 2-5 psi), a
arbitrary identification number (e.g. 1)
Justin, thank you.
I have implemented the pull code but that also exhibits the same error when
I use 12 cores (failed at about 2ns) and the simulation goes on fine when I
use 6 cores (now at about 32 ns).
I tried using the v-rescale thermostat (instead of Nose-Hoover) and
Parinello-Rahman
Hi gmx users!
I am using gmx2019.4 in centos 7.6 (gcc version 4.8.5), the MD was conducted
successfully. However, when I proceeded the PCA analysis, there was a wrong in
the output informations.
command:
echo 3 3|gmx covar -f md_res_center_mol_fit_protein.xtc -s ../md.tpr -o
eigenvalues.xvg
