Script assumes that variable $distance is the second row separated by space in
the file dist{number}.xvg which appears after execution of system call
gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg
-select \'com of group \"lig\" plus com of group \"protein\"\'I just t
Hi,
See http://www.gromacs.org/Documentation/How-tos/Position_Restraints. And
do manage the spelling of the abbreviation correctly!
Mark
On Mon, 4 Sep 2017 06:27 Dilip H N wrote:
> Hello,
> I am running a peptide simulation, i have done an energy minimization , now
> going to do nvt/npt simula
Hello,
I am running a peptide simulation, i have done an energy minimization , now
going to do nvt/npt simulation...
My doubts are:-
1] Why is the position restrained (-DPORSE)in the nvt/npt mdp files..??
2] If i remove the -DPORSE than i can see the molecules moving , but with
option -DPORSE, the
Hello Gmx user,
I would like to transport solute molecule from the ion channel (intracellular
to extracellular site) using steered MD and umbrella sampling method to
calculate the energy.
I followed Dr. Lemkul's tutorial and it works fine upto equilibration step but
in distance.pl it shows s
Hello Gmx user,
I would like to transport solute molecule from the ion channel (intracellular
to extracellular site) using steered MD and umbrella sampling method to
calculate the energy.
I followed Dr. Lemkul's tutorial and it works fine upto equilibration step but
in distance.pl it shows s
