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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