Hi Esteban and Vitaly, Thanks for your respose, I tried "trjconv" with -pbc mol while generating movie and it worked this time.
regards, vivek On 12 July 2010 16:01, Vitaly Chaban <[email protected]> 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. > -- > 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 >
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