[gmx-users] about -CN triple bond

[C.Y. Chang]

Hi,

I have tried to add

[ position restraints ]
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.

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

Fatal error:
Invalid dihedral type 1000


                                          Chia-yun


2011/2/18 Mark Abraham <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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