[gmx-users] Re: MD run for octanol system

vivek sharma viveksharma.iitb at gmail.com
Thu Jul 15 07:14:08 CEST 2010

Hi Esteban and Vitaly,
Thanks for your respose, I tried "trjconv" with -pbc mol while generating
movie and it worked this time.


On 12 July 2010 16:01, Vitaly Chaban <vvchaban at gmail.com> wrote:

> Hmm... Straight lines... Is it VMD that your used to visualize the
> trajectory?
> I think this is just due to PBC. Compute some RDFs and they will give
> you an answer if your system is healthy.
> Dr. Vitaly Chaban
> > 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.
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