[gmx-users] about -CN triple bond

C.Y. Chang chiayun.chang at gmail.com
Fri Feb 18 03:13:49 CET 2011


I am dealing with the lipid bilayer permeation simulation.
Most compounds can be finished, but the compounds with CN can't be performed
I have searched the discussion in the gmx-users discussion.
The "vsite" has been mentioned, and I have refered to the gromacs manual.
But I don't understand that how I can use the "vsite".
(add the toplogy file or use the command line?)
I attach the PDB and toplogy file of the molecule.
First, I performed the molecular dynamic simulation for the pure lipid
bilayer, and the step was been finished.
After I insert the molecule, these command lines are performed.

grompp -f minim.mdp -c cmplx.pdb -p topol_dppc.top -o em.tpr
mdrun -v -deffnm em
grompp -f npt_cmplx.mdp -c em.gro -p topol_dppc.top -o npt_cmplx.tpr
nohup mdrun -v -deffnm npt_cmplx &

Thanks for your help.

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