[gmx-users] about -CN triple bond

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 18 07:41:36 CET 2011

On 18/02/2011 1:13 PM, C.Y. Chang wrote:
> Hi,
> I am dealing with the lipid bilayer permeation simulation.
> Most compounds can be finished, but the compounds with CN can't be 
> performed simulation.
> 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".

The theory is discussed in chapter 4 and there's a brief example in 
5.2.2. What have you tried and what went wrong?


> (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.
> Best,
>                                                                         Chia-yun

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