[gmx-users] NEUTRALISED CHARGES

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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.akalabya at gmail.com <mailto:bissoyi.akalabya at gmail.com>
>         <mailto:bissoyi.akalabya at gmail.com
>         <mailto:bissoyi.akalabya at 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
> 
>            _______________________________________________
>            gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>            <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> 
>            http://www.gromacs.org/mailman/listinfo/gmx-users
>            Please search the archive at http://www.gromacs.org/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
>         <mailto:gmx-users-request at gromacs.org>
>            <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>.
> 
>            Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
>         ------------------------------------------------------------------------
> 
> 
>         _______________________________________________
>         gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         http://www.gromacs.org/mailman/listinfo/gmx-users
>         Please search the archive at http://www.gromacs.org/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
>         <mailto:gmx-users-request at gromacs.org>.
>         Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
>     -- 
>     ========================================
> 
>     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
> 
>     ========================================
> 
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/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
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

-- 
========================================

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

========================================