[gmx-users] about -CN triple bond
C.Y. Chang
chiayun.chang at gmail.com
Tue Mar 1 06:58:44 CET 2011
Hi,
I have modified the dummy atom in the topology (attached files) and pdb
file.
On the other side, I study the lipid system.
Therefore, I constrained all bond lengths in my system.
This is bond parameters in the mdp file.
continuation = no ; starting up
constraints = all-bonds ; constrain all bond lengths
constraint-algorithm = lincs ; holonomic constraints
lincs-iter = 1 ; accuracy of LINCS
lincs-order = 4 ; also related to accuracy
But the MDS process was performed and it showed the error msg.
ERROR: Cannot have constraint (2-1) with virtual site (2)
ERROR: Cannot have constraint (2-3) with virtual site (2)
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: vsite_parm.c, line: 856
Fatal error:
There were 2 virtual sites involved in constraints
-------------------------------------------------------
How should I solve the problem.
Thanks for your suggestions.
Chia-yun
Chang
2011/2/28 Mark Abraham <mark.abraham at anu.edu.au>
>
>
> On 02/28/11, *"C.Y. Chang" * <chiayun.chang at gmail.com> wrote:
>
> 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.
>
>
> Solving the problem requires removing the one of the three existing
> co-linear atoms by treating it as a virtual atom. You haven't done that.
> You've introduced a fourth co-linear atom - the dummy. Treat the central C
> atom as a dummy. That reduces your number of non-virtual co-linear atoms to
> 2 in all cases. That solves this problem.
>
> Mark
>
>
>
> 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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>
>
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