Actually my final .gro file is totally broken into smaller parts when i load it in vmd, for this what will i do?
On Sat, Sep 9, 2017 at 7:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/9/17 10:05 AM, ISHRAT JAHAN wrote: > >> Dear Justin >> commands which i have used are given belown- >> gmx trjconv -f protein_out.xtc -s protein_md.tpr -o protein_nojump.xtc >> -pbc >> nojump >> gmx trjconv -f protein_nojump.xtc -s protein_md.tpr -o protein_cluster.xtc >> -pbc cluster >> gmx trjconv -f protein_cluster.xtc -s protein_md.tpr -o protein_pbc.xtc >> -pbc whole -center -n protein_drg.ndx >> >> > Check the link I provided. You're going out of order so you're probably > going to end up with an incorrect representation. > > -Justin > > > On Sat, Sep 9, 2017 at 7:04 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 9/9/17 1:50 AM, ISHRAT JAHAN wrote: >>> >>> Dear all, >>>> I have done 100ns md simulation of protein with drug using amber99sb.ff >>>> with gromacs-5.1.4 version. After simulation i found my protein broken >>>> into >>>> smaller parts in .gro file but when i load the final xtc file to pr.gro >>>> molecule does not break. I have applied -pbc nojump ,cluster and whole >>>> but >>>> unable to solve the problem. >>>> Will anyone help me to solve the above problem. >>>> >>>> >>> We'll need to see your commands, exactly as issued, to be able to say >>> anything. In general: >>> >>> http://www.gromacs.org/Documentation/Terminology/Periodic_ >>> Boundary_Conditions#Suggested_trjconv_workflow >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> ================================================== >>> -- >>> 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. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > -- > 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. > -- 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.