[gmx-users] about -CN triple bond

C.Y. Chang chiayun.chang at gmail.com
Mon Feb 28 08:59:32 CET 2011 

Hi,

I try to add a dummy atom in my small molecular pdb and topology file.
(attached files)
But the MDS process still shut down.
The msg. is
[1]+  Exit 255                nohup mdrun -v -deffnm npt_cmplx
Could you give me some suggestions for dealing with the problem.
Thaks a lot.
Best,


                         Chia-yun Chang


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

>  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>
>
>>  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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>
>
>
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