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.abra...@anu.edu.au
<mailto:mark.abra...@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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