Thanks On Sat, Feb 15, 2020, 8:02 PM Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 2/15/20 4:50 AM, Devargya Chakraborty wrote: > > i want to calculate the order prameter between two carbon atom namrd C01 > > and C03 in my topology file but while calculating, i am getting the > > following error. > > gmx order is designed to compute deuterium order parameters in alkyl > chains. It requires special index groups that only contain the atoms of > interest and those flanking them to define the local molecular axis. See > http://www.mdtutorials.com/gmx/membrane_protein/09_analysis.html for an > example. > > -Justin > > > Taking z axis as normal to the membrane > > Reading file nvt.tpr, VERSION 2019.1 (single precision) > > Using following groups: > > Groupname: System First atomname: C01 First atomnr 0 > > Groupname: Other First atomname: C01 First atomnr 0 > > Groupname: EMI First atomname: C01 First atomnr 0 > > Groupname: NSC First atomname: NBT First atomnr 760 > > Groupname: Water First atomname: OW First atomnr 1360 > > Groupname: SOL First atomname: OW First atomnr 1360 > > Groupname: non-Water First atomname: C01 First atomnr 0 > > Groupname: C01 First atomname: C01 First atomnr 0 > > Groupname: C04 First atomname: C04 First atomnr 1 > > Groupname: C03 First atomname: C03 First atomnr 2 > > Groupname: H07 First atomname: H07 First atomnr 3 > > Groupname: H09 First atomname: H09 First atomnr 4 > > Groupname: H08 First atomname: H08 First atomnr 5 > > Groupname: C05 First atomname: C05 First atomnr 6 > > Groupname: H0B First atomname: H0B First atomnr 7 > > Groupname: H0C First atomname: H0C First atomnr 8 > > Groupname: H0D First atomname: H0D First atomnr 9 > > Groupname: N00 First atomname: N00 First atomnr 10 > > Groupname: C06 First atomname: C06 First atomnr 11 > > Groupname: H0F First atomname: H0F First atomnr 12 > > Groupname: C0N First atomname: C0N First atomnr 13 > > Groupname: H0O First atomname: H0O First atomnr 14 > > Groupname: H0P First atomname: H0P First atomnr 15 > > Groupname: H0Q First atomname: H0Q First atomnr 16 > > Groupname: N02 First atomname: N02 First atomnr 17 > > Groupname: H0E First atomname: H0E First atomnr 18 > > Groupname: NBT First atomname: NBT First atomnr 760 > > Groupname: SBT First atomname: SBT First atomnr 761 > > Groupname: OBT First atomname: OBT First atomnr 763 > > Groupname: CBT First atomname: CBT First atomnr 764 > > Groupname: F1 First atomname: F1 First atomnr 768 > > > > Reading frame 0 time 0.000 Number of elements in first group: > > 10360 > > > > ------------------------------------------------------- > > Program: gmx order, version 2019.1 > > Source file: src/gromacs/gmxana/gmx_order.cpp (line 546) > > > > Fatal error: > > grp 1 does not have same number of elements as grp 1 > > > > can anybody help. > > > > Thanks > > -- > ================================================== > > 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. > -- 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.