Amit Choubey wrote:
On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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>
==============================__==========
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========================================
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
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