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. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
