[gmx-users] how to simulate a line charge
Justin A. Lemkul
jalemkul at vt.edu
Sat Aug 13 06:16:38 CEST 2011
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.
> 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
> 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 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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