[gmx-users] Erro in SMD simulation..

[Kalyanashis]

Thank you so much Justin. Now I am trying with a rectangular box. I don not
whether it will work or not.


On Tue, Apr 1, 2014 at 10:51 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5015553h30 at n6.nabble.com> wrote:

>
>
> On 4/1/14, 12:56 PM, Kalyanashis wrote:
>
> > Thank you Justin for your valuable reply. But you know, my box size is
> > 17.744*17.744*17.744 nm^3. I have used "editconf -bt cubic -f
> > 20-SCH-edit1.pdb -o 20-SCH-edit2.pdb -c -d 1.6" to generate the box.
>  And
> > the full description of the box size I have used is
> > "Read 15484 atoms
> > No velocities found
> >      system size :  7.604  8.101 13.546 (nm)
> >      diameter      : 14.544               (nm)
> >      center         :  2.405  3.212 -2.870 (nm)
> >      box vectors  :  0.000  0.000  0.000 (nm)
> >      box angles   :   0.00   0.00   0.00 (degrees)
> >      box volume  :   0.00               (nm^3)
> >      shift             :  6.467  5.661 11.742 (nm)
> > new center       :  8.872  8.872  8.872 (nm)
> > new box vectors : 17.744 17.744 17.744 (nm)
> > new box angles  :  90.00  90.00  90.00 (degrees)
> > new box volume  :5587.13               (nm^3)"
> > Please suggest me the better option for my system. Should I increase the
> d
> > value? Actually, the whole system contains approximately 193000 atoms
> and
> > whenever I am increasing the d value the atoms no. is increasing
> > significantly. Is there any option which can allow me to increase the
> box
> > size without increasing the number of solvent molecules?  And one more
> more
> > thing, is the cubic option fine?
>
> You're using pressure coupling so the box vectors change over time.  The
> error
> complains because 8.662854 * 2 = 17.325708, which is totally feasible to
> expect
> for normal box vector fluctuations.
>
> A cubic box is usually the most inefficient shape for most systems.
>  Depending
> on the symmetry of your system, you can probably do a lot better.  If
> you're
> pulling only along z, then a rectangular box with a suitable z-dimension
> is
> probably the next easiest way to go and will save you a ton of unnecessary
> water
> molecules.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> [hidden email] <http://user/SendEmail.jtp?type=node&node=5015553&i=0> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to [hidden email]<http://user/SendEmail.jtp?type=node&node=5015553&i=1>.
>
>
>
> ------------------------------
>  If you reply to this email, your message will be added to the discussion
> below:
>
> http://gromacs.5086.x6.nabble.com/Erro-in-SMD-simulation-tp5015535p5015553.html
>  To start a new topic under GROMACS Users Forum, email
> ml-node+s5086n4370410h97 at n6.nabble.com
> To unsubscribe from Erro in SMD simulation.., click here<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=5015535&code=a2FseWFuLmNoZW0uaW5AZ21haWwuY29tfDUwMTU1MzV8NTkxMDYyNTYz>
> .
> NAML<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>



-- 
Kalyanashis Jana
email: kalyan.chem.in at gmail.com


--
View this message in context: http://gromacs.5086.x6.nabble.com/Erro-in-SMD-simulation-tp5015535p5015556.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.