[gmx-users] MD run for octanol system

[Esteban Gabriel Vega Hissi]

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

Esteban
--

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
>
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