[gmx-users] about -CN triple bond

[Mark Abraham]

On 19/02/2011 5:18 PM, C.Y. Chang wrote:
> 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 ]

That's misspelled too. Underscores are significant. You have to be 
literal when dealing with computers.

> ; Site from funct a
> 5 1 2 1 0.7439756
>
> What should I choose the vsite for the -CN group? (2, 3fd or others?)

The problems come when the force from normal angle and dihedral 
functions aren't numerically stable when there are 3 collinear atoms. 
The way to avoid this is to have one of those atoms "virtual". Forces on 
it get projected onto the real atoms from which it is defined, the 
integration of forces proceeds only on the real atoms, and the position 
of the virtual site gets reconstructed later. So, which type do you 
think will work best here?

> I read the manual and the columns of the vsite need some parameters.
> The "Site" seems to be the atom number.

Yes.

> The "from" seems some atom group, but which atoms should be included?

The real atoms that form the virtual site. The number and order depends 
on the type of virtual site. Which atom is which is covered back in 4.7 
You need to read that together with 5.2.2, like I said several emails ago.

> How could obtain the "func" values?

That's situation-dependent. Here, you want to pick a position along the 
line that will lead to the three atoms being a sensible distance apart.

> Could you give me a molecule for my example?

No, I don't have one. Your example above will construct atom 5 from 1 
and 2 75% of the way along the line from 1 to 2, per Figure 4.16 and 
equation 4.134.

Mark

> Thanks for your help.
>
> Best,
>
>                                                         Chia-yun
>
>
> 2011/2/19 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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
>>     <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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>
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