[gmx-users] MD run for octanol system

Esteban Gabriel Vega Hissi egvega at gmail.com
Mon Jul 12 12:00:48 CEST 2010

try converting (trjconv) your trajectory using the flag "-pbc res" or "-pbc


On Mon, Jul 12, 2010 at 8:45 AM, vivek sharma <viveksharma.iitb at gmail.com>wrote:

> Hi There,
> I am trying to run MD simulation for octanol using GROMACS, I have
> downloaded the octanol.tar.gz from the user contributed section
> http://www.gromacs.org/@api/deki/files/18/=octanol.tar.gz.
> When I performed this MD run according to the run input file and molecule
> topology provided in this download, I observed straight lines in the system
> while visualizing the trajectory. Can anybody suggest if there is any
> problems in the run parameters provided or it is some mistake at my part ?
> As a first thought It seems like a boundary condition problem to me. Any
> insight into this will be really helpful for me.
> Is there any other source for getting required information for octanol.
> My final target is to run MD in water/octanol box. Please guide me with dos
> and donts, If anybody has attempted for the same.
> Thanks in advance!!!
> regards,
> Vik
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100712/6dccf677/attachment.html>

More information about the gromacs.org_gmx-users mailing list