[gmx-users] Linear CG beads, grompp doesn't work

[Xu Dong Huang]

@Justin,

Does the philosophy described in your tutorial apply to CG martini bead models where 1 bead describes the entire CO2 atom? (If I were to do that, assuming) 


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudongh at eden.rutgers.edu 

On Jan 1, 2013, at 10:46 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:

> Dear Justin,
> 
> My .itp does not contain angles or dihedrals because we are simply interested in the very simple generic case of a linear (what we assume by defining a coordinate file of linear beads) polymer model. I will go through the tutorial and try to see if it resolves my issue. 
> 
> 
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering 
> xudongh at eden.rutgers.edu 
> 
> On Jan 1, 2013, at 10:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
>> 
>> 
>> On 1/1/13 10:33 PM, Xu Dong Huang wrote:
>>> Dear advanced gromac users,
>>> 
>>> I am trying to simulate a long linear chain of polymer using CG beads. (about 200 beads), all with same type charge interactions. (examples shown:) I read on previous gromacs mailing list that linear systems with same charges make the system unstable? But is there anyway to go around that?
>>> 
>> 
>> It's the angles that make the system unstable.  One can use virtual sites to get around the issue.  There is a trivial example in a tutorial I wrote:
>> 
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html
>> 
>> The bigger question is whether or not the angles in the molecule impose linearity, or whether the initial configuration is simply a line of particles that may deviate according to angle and dihedral potentials.  You haven't shown the [angles] or [dihedrals] directives, so it's not clear what you're intending, exactly.
>> 
>>> [atoms]
>>> 1	P3	O1	mon	1	0.00
>>> 2	P3	O1	mon	2	0.00
>>> 3	P3	O1	mon	3	0.00
>>> 4	P3	O1	mon	4	0.00
>>> 5	P3	O1	mon	5	0.00
>>> 6	P3	O1	mon	6	0.00
>>> 7	P3	O1	mon	7	0.00
>>> 8	P3	O1	mon	8	0.00
>>> 9	P3	O1	mon	9	0.00
>>> …….
>>> [ bonds ]
>>> 1	2	1	0.43	17000
>>> 2	3	1	0.43	17000
>>> 3	4	1	0.43	17000
>>> 4	5	1	0.43	17000
>>> ……
>>> 
>>> However, when i do grompp -f vac_min.mdp -c mon.gro -p mon.top -o vac.tpr
>>> -it returns the error of:
>>> Fatal error:
>>> The largest charge group contains 200 atoms. The maximum is 32.
>>> For more information and tips for troubleshooting, please check the GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> 
>>> Please let me know if there is a way to go around that. Thank you.
>>> 
>> 
>> Do as the error message says and put fewer than 32 atoms in each charge group. The size of the charge group has implications for neighbor searching if using a group-based cutoff scheme.
>> 
>> -Justin
>> 
>> -- 
>> ========================================
>> 
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> 
>> ========================================
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