[gmx-users] about -CN triple bond
Mark.Abraham at anu.edu.au
Sat Feb 19 05:07:56 CET 2011
On 19/02/2011 3:02 PM, C.Y. Chang wrote:
> 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.
> 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:
> 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
> nohup mdrun -v -deffnm npt_cmplx &
> Thanks for your help.
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