Hi Satya, You can use trjorder to rearrange solvent molecules in your structure file, according to distance. Then you can replace the first x solvent molecules by hydroxyl. Actually you only need to remove a hydrogen atom per water...
Hope it helps, Tsjerk On Thu, Jul 5, 2012 at 5:04 AM, SatyaK <mail2mvsku...@yahoo.com> wrote: > > Thanks once again Mark. I am trying to figure out things. Basically, I am > using ReaxFF for my simulations. The basic problem I want to address is, to > place OH radicals as close as possible to the DNA and rest with water > molecules in a box. > > Thanks, > Satya. > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/DNA-simulations-tp4998988p4999093.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
