[gmx-users] about -CN triple bond

[Mark Abraham]

On 19/02/2011 3:02 PM, C.Y. Chang wrote:
> Hi,
>
> I have tried to add
>
> [ position restraints ]

This is misspelled. Surely grompp warned about this?

> 2 1 1000 1000 1000 ; Restrain to a point
> 1 1 1000 0 1000 ; Restrain to a line (Y-axis)
> 3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane)
>
> in the end of the topology file.

This does not even approach the solution to your problem. Position 
restraints inhibit diffusion and structural changes. You need a vsite, 
like you knew earlier.

> In the em. process, I get the eroor msg.

No, this error happened in grompp.

> Fatal error:
> Invalid dihedral type 1000

GROMACS didn't recognise the mis-spelled directive, and so it's trying 
to make sense of your position restraint lines as dihedrals.

Mark

>                                           Chia-yun
>
>
> 2011/2/18 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>
>     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?
>
>     Mark
>
>
>         (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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