[gmx-users] about -CN triple bond
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Mar 1 07:37:42 CET 2011
On 1/03/2011 4:58 PM, C.Y. Chang wrote:
> 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.
You made a virtual atom 2 three-quarters of the way from real atoms 1
and 3 (is an N-C bond really three times as long as an C#N bond?). You
defined bonds between 1 and 2, and between 2 and 3. Then you told
GROMACS to convert them into constraints. It didn't like that.
So remove those bonds, and make a bond between 1 and 3 whose equilibrium
length is the sum of those of the old bonds. The force constants won't
matter, since you're holding the length fixed anyway (but you may as
well interpolate between the previous two force constants). You will
need to adjust your angle and dihedral definitions accordingly -
references to atom 2 now need to be to atom 1.
Mark
> Thanks for your suggestions.
>
>
> Chia-yun Chang
>
>
> 2011/2/28 Mark Abraham <mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>>
>
>
>
> On 02/28/11, *"C.Y. Chang" * <chiayun.chang at gmail.com
> <mailto: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
>> <mailto: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
>>> <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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>>
>>
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