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

[Xu Dong Huang]

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
> 
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists