[gmx-users] how to simulate a line charge

[Justin A. Lemkul]

Amit Choubey wrote:
> 
> 
> On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Amit Choubey wrote:
> 
>         Hi all,
> 
>         I am trying to do a calculation on an artificial line charge in
>         vacuum. The line charge has 267 atoms and each atom has a 1e
>         charge. The atoms are bonded by a bond term and an angle term. I
>         defined the required itp
> 
> 
>     If you're trying to keep the atoms in a line, the system will not be
>     stable. Angles of 180 degrees routinely crash.
> 
> 
> Not even if i use a 3 body angle term with equilibrium angle = 180? If 
> not then why ?
> 

The code has had problems dealing with this case.  I do not know if there have 
been any improvements.  The only really stable way to induce linearity is 
through virtual sites, but I don't know if it is possible to create several 
hundred virtual interactions defined along a line.

-Justin

> 
> 
>         files and top file. When i issue
> 
>         grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp
> 
>         I get the following error message.
> 
>         Program grompp_jpt, VERSION 4.5.3
>         Source code file: grompp.c, line: 175
> 
>         Fatal error:
>         The largest charge group contains 267 atoms. The maximum is 32.
>         For more information and tips for troubleshooting, please check
>         the GROMACS
>         website at http://www.gromacs.org/__Documentation/Errors
>         <http://www.gromacs.org/Documentation/Errors>
> 
>         What should i try to do to circumvent this error.
> 
> 
>     The maximum charge group size is defined in the
>     include/types/nblist.h header. You can alter the value there, which
>     will get around the error, but consider whether or not this is even
>     a good physical model.  If all atoms are in the same charge group,
>     there are no electrostatic interactions between these atoms since
>     neighbor searching is done and short-range energies are calculated
>     based on inter-charge group distances.  I have no idea how to
>     properly simulate a line of positively-charged particles, but be aware.
> 
> 
> Thanks for the pointer and the awareness remark. But since this is a 
> model system and for the physical problem i am trying to deal with its 
> alright if the atoms within the line charge do not interact via 
> non-bonded potentials.
>  
> 
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/__mailman/listinfo/gmx-users
>     <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>     Please search the archive at
>     http://www.gromacs.org/__Support/Mailing_Lists/Search
>     <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
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================