Marius Retegan wrote:
There is a log attached in the first e-mail.
My first reaction was the same. Why 14 :).
Ah, that would make sense. May I suggest a tip to all users: don't send
attachments when it is just as simple to copy and paste text into an email. I
often see small attachment files in emails (footers, images, etc) so I ignore
them. Also, don't send attachments without extensions. Names like "system"
might look suspicious (especially someone like me who is cautious, knowing
nothing about the level of security on your machine). Use obvious names, like
"output.log" or something, if you must.
But yes, 14 is indeed correct in this case :)
-Justin
Marius
On Mon, Apr 6, 2009 at 1:10 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Pawan Kumar wrote:
Hi,
You should add 14 cl ions.
Why 14? The number of Cl- ions that are necessary is pretty much
spelled out by grompp, and the net charge of the system is printed
in the .top (qtot section in [atoms]). If your system has a net
charge of +2, add 2 Cl- ions, and so forth.
-Justin
Regards,
Pawan
On Mon, Apr 6, 2009 at 12:26 PM, akalabya bissoyi
<bissoyi.akala...@gmail.com <mailto:bissoyi.akala...@gmail.com>
<mailto:bissoyi.akala...@gmail.com
<mailto:bissoyi.akala...@gmail.com>>> wrote:
hello gromacs
i am trying to minimise my protein-ligand complex in
gromacs.but it
shows that system has non zero charge
can any body says how much *cl ion*, i have to add to neutralised
it. i am terminal window text.
thank u
-- AKALABYA BISSOYI
N.I.T.Rourkela
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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