On 7/11/12 6:19 AM, amir abbasi wrote:
Thanks Justin,
But I want to neutralize my system in implicit solvent.
In Amber I had use Debye screening but in gromacs I don't know what should I do.
From my understanding, this remains an unresolved issue.
-Justin
On Wed, Jul 11, 2012 at 2:45 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
On 7/11/12 6:00 AM, amir abbasi wrote:
Hi All!
I want to use Implicit solvent to simulate a nucleic acid sequence.
How can I do it?
I use this command:
genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname
CL -neutral -conc 0.1
ions.tpr file is same as umbrella sampling tutorial.
I got this error message:
Fatal error:
Your solvent group size (2898) is not a multiple of 31
what should I do?
One does not typically add explicit ions in an implicit solvent system.
genion fails because it appears you are trying to replace parts of your
nucleic acid with ions.
-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
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========================================
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
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