<br><br><div class="gmail_quote">On Sat, Dec 27, 2008 at 6:36 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d">Quoting Manik Mayur <<a href="mailto:manik.mayur@gmail.com">manik.mayur@gmail.com</a>>:<br>
<br>
> On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur <<a href="mailto:manik.mayur@gmail.com">manik.mayur@gmail.com</a>> wrote:<br>
><br>
> > Hi all,<br>
> ><br>
> > I have a few probIems/confusions and will be extremely thankful for any<br>
> > help. I added some "Cl- ions" by replacing water using "genion (and -nn)".<br>
> > It generated a "topol.top" file with Cl listed in [ molecules ]. Now when I<br>
> > try to run grompp, it gives an error saying "no such molecule type Cl". So<br>
> > my questions are:<br>
<br>
</div>Exact command lines are much more useful than your interpretation of what you<br>
typed. If you just used genion -nn, that's probably insufficient information.<br>
</blockquote><div class="Ih2E3d"><br>Sorry for the confusion but genion won't add "Cl-" on its own unless I provide it with the relevant options (providing which I thought would be impertinent here). The only concern here was to find out "why Cl was listed in the [ molecules ] section of the topol.top file", hence the error as no such molecule was defined.<br>
<br>But I found a workaround as to generate a .pdb file using genion, and then use pdb2gmx to generate .gro and topol.top files, which I see automatically generates a .itp file corresponding to "Cl-" and #includes it in topol.top apart from adding it into [ molecules ] section. So now its working but the question no. 3 is still on :)<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
> > 1) How to avoid that error? Do I have to define a Cl.itp and add molecule<br>
> > type etc. ?<br>
<br>
</div>Check ions.itp for the proper ion nomenclature for whatever force field you're<br>
using. Different force fields use different naming.</blockquote><div><br>ok<br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<div class="Ih2E3d"><br>
> > 2) If I try to add Cl using -neutral option (as my system before already<br>
> > had a net +ve charge), it says "No ions to add and no potentials to<br>
> > calculate", why?<br>
<br>
</div>Probably because your command line was just genion -neutral, right? You didn't<br>
tell genion what type of ions to add, so it's not going to do anything; it's<br>
not magic!<br>
</blockquote><div class="Ih2E3d"><br>Again sorry for the confusion(and I know its not magic :)) but "apart" from providing the ion name to be added etc., according to the manual, you can add ions by following ways-<br>
1) provide no. of ions to be added by -nn.<br>2) use -neutral so that if the system already has a net charge, that will be compensated.<br>3) use -conc.<br>The first one works, but the second one is giving the above mentioned error.<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
> > 3) Why is Cl listed in molecules and not [atoms] section?<br>
<br>
</div>If you properly #include "ions.itp" then it is an additional moleculetype<br>
definition within the topology.<br>
<div class="Ih2E3d"><br>
> > 4) If I wish to use SPC/E model, do I have to use ffgmx*. I tried using<br>
> > ffG43a1* with #include "spce.itp" in topol.top. Is that correct? what else<br>
> I<br>
<br>
</div>You should not use ffgmx for anything. Using #include "spce.itp" is correct for<br>
use with other force fields.<br>
</blockquote><div class="Ih2E3d"><br>ok<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
> > would have to do?<br>
> > 5) Is it mandatory to have periodicity=xyz with coulumb-type=PME and ewald<br>
> > geom=3dc, other than using walls option(I have my own channel walls in the<br>
> > system, so want to avoid them). Is there a way to use periodicity=xyz with<br>
> > coulumb-type=PME and ewald geom=3dc?<br>
> ><br>
> Is there a way to use periodicity=xy with coulumb-type=PME and ewald<br>
> geom=3dc?<br>
> ><br>
<br>
</div>I can't comment on this specifically, but have you tried it? Does it give some<br>
sort of error message if you do?</blockquote><div> </div>I tried using above but grompp says its not possible. Meanwhile, I read in a paper(JCP2003(118),4692-4701) that they used a modified PME with 3 times bigger box dimension in the z-direction than the slab geometry. And I am using it with periodicity=xyz turned on.<br>
<br>So unless I use walls, I can't use periodicity=xy with coulumb-type=PME and ewald_geom=3dc, Is that right?<br><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
-Justin<br>
</blockquote><div class="Ih2E3d"><br>Thanks,<br>Manik<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
> > Thanks,<br>
> > Manik<br>
> ><br>
> > --<br>
> > _________________<br>
> > HAPAX LEGOMENA<br>
> ><br>
><br>
><br>
><br>
> --<br>
> _________________<br>
> HAPAX LEGOMENA<br>
><br>
<br>
<br>
<br>
</div>========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/</a><br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>_________________<br>HAPAX LEGOMENA<br>