[gmx-users] how to simulate a line charge

[Amit Choubey]

On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul <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 ?


>
>  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 | (540) 231-9080
> 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
> 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.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110812/e51742ba/attachment.html>