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

[Vitaly Chaban]

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.