Meyer-Almes, Franz-Josef, Prof. Dr. wrote:
Dear all,
I have two question:
1) Are the atom types I chose for the use of OPLS force field correct?
I use gromacs 4.0.7 with opls force field under Ubuntu Linux to simulate
enzyme drug interaction. Since the Dundee Prodrg Server conver
Dear all,
I have two question:
1) Are the atom types I chose for the use of OPLS force field correct?
I use gromacs 4.0.7 with opls force field under Ubuntu Linux to simulate enzyme
drug interaction. Since the Dundee Prodrg Server converts PDB files of drug
structures just in an .itp file comp
Probably means that atoms are moving across the pbc boundary from one
side of the box to another. The visualiser you are using is trying to
maintain the bond between the atoms after the move, so draws it all the
way across the box itself. Two ways to fix, don't visualise the bonds,
using either p
Thanks Itamar for your reply, but the tube actually does not jump, but
the lines showing the bonds start to show bonding between
non-neighbouring atoms, i.e., the hexagonal shape characteristic of
nanotubes is destroyed, and it starts from the third frame regardless of
the start time. I tried t
Shalom George
Maybe your nanotube 'jump' over the PBC?
Try 'trjconv -pbc whole ...'
Best,
Itamar
George Abadir wrote:
Hi,
I finished a simulation of a carbon nanotube in water. I made a
movie of the simulation using 'trjconv' to view with Pymol. The problem
is that starting from the thi
Hi,
I finished a simulation of a carbon nanotube in water. I made a
movie of the simulation using 'trjconv' to view with Pymol. The problem
is that starting from the third frame it messes the carbon nanotube
bonds. I changed the start time and again in the third frames it messed
things up.
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