Thank you so much Prof. Lemkul for your reply. As I don't know what and how to use this pull code, if you have any idea regarding what you have suggested will be of great help to me. Meanwhile I will read more about it.
Thank You On Mon, Apr 20, 2020 at 1:14 AM Justin Lemkul <jalem...@vt.edu> wrote: > [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible > for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule > <https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Fkey%3D6r1aiDRAExonCQQ46dpwnd9FXqjY72Y8Po42hVlnInE%253D%26token%3DTgdaxblawl%252FgVeD8m4SXxHim9ynSCDUT7CT9o1aZrV%252FvxooXjJWAjL14DVylDrrQb3AYJQpWlXvpqqIa8Sccw2apChErnWaNWp4kmKV4nUUIGOj2FcqxmUzOCCulZIvnx9Y%252Fn38jPm4%253D&tc_serial=52395970044&tc_rand=272183213&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001> > | More info > <http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=52395970044&tc_rand=272183213&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001> > > > On 4/18/20 4:43 AM, Shashank Ranjan Srivastava wrote: > > Hello everyone, > > I want to create a gap between the first and last strand of a beta > barrel > > so that I can put a new strand in between. > > So, I have generated an input file using charmm-gui and using its gromacs > > production file (production.mdp) to run the simulation. I want to use a > > harmonic wall model to disrupt the bonding between the first and last > > strand of the beta barrel but not getting how to do it . > > I have asked it before as well but I did not get any suggestion. > > Please kindly help me with this query if anybody has any idea regarding > > this. > > I suggest using the pull code. The implementation of walls in GROMACS > does not do what you're asking. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Shashank Ranjan Srivastava Molecular Biophysics Laboratory Department of Biological Sciences, IISER-Bhopal, Madhya Pradesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
