[gmx-users] MD run for octanol system

vivek sharma viveksharma.iitb at gmail.com
Mon Jul 12 08:45:49 CEST 2010

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
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!!!

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