[gmx-users] about -CN triple bond

[C.Y. Chang]

Hi,

The errpr msg. that I expressed in the previous mail is unclear.
It really happened in the grompp step of my dealinw with the em.
The manual shows that the viste can be used by

[ virtual sites2 ]
; Site from funct a
5 1 2 1 0.7439756

What should I choose the vsite for the -CN group? (2, 3fd or others?)
I read the manual and the columns of the vsite need some parameters.
The "Site" seems to be the atom number.
The "from" seems some atom group, but which atoms should be included?
How could obtain the "func" values?
Could you give me a molecule for my example?
Thanks for your help.

Best,

                                                        Chia-yun


2011/2/19 Mark Abraham <Mark.Abraham at anu.edu.au>

>  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>
>
>> 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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>
>
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