hi, Justin. Thank you for your meticulous and patient explanation ! Before I see this post, I misunderstood the meaning of sharing bonds. I thought note only the bonds,but also the angles and the dihedrals should be added to top file.
It was so complicated to deal manually that I wrote that script. I will read the doucment you mentioned carefully . And I will fix these notes and warnings as grompp and mdrun suggest. Thank you for your help ! Cun Zhang > Again, heed the note. I cannot think of a solid reason for a modern > simulation > being conducted using cutoff electrostatics, unless the goal is to prove that > such a method is less accurate than a more modern technique like PME. Again, > these notes are your friend. I see that they return during your PR attempts. > You should not ignore the advice that grompp is giving you. The artifacts of > plain cutoffs are well-documented. > Cun Zhang wrote: > > <snip> > >> I hope generate sharing bonds between the atoms at the top edge and the >> atoms at the bottom edge of CNT by x2top. But the parameter -pbc does >> not work. So I add 4 layers at the top of CNT.pdb and rename it >> CNT_new.pdb, that is, the front 832 rows of them are same. >> >> The atoms of No. 833-960 in CNT_new.pdb can be seen the bottom 4 layers >> of atoms of No.1-128 of CNT.pdb translated up a box hight. So after >> generating the topology file and renaming atoms of No. 833-960 to >> No.1-128 in the topology file (use the command 'x2top -nopbc') the >> topology file of CNT_new.pdb should be the same as the topology file of >> CNT.pdb with sharing bonds (and angles, diherals) ( use the command >> 'x2top -pbc' ). >> > > This still makes no sense to me at all. You're creating duplicate atoms at > one > end of the structure to make them have the same atom numbers of those at the > other end of the molecule? Forgive my confusion, I simply don't know what > you're doing. The concept of bonding is not that parameters are "shared," it > is > the following: > > Consider atoms A and Z, residing at the "ends" of a CNT, as shown here (with > vertical lines indicating the boundaries of the unit cell): > > | | > | A . . . . . . . Z | > | | > > You simply need to define a bond in the topology between A and Z, no > renumbering > or fancy tricks required, just add the bond to the [bonds] directive: > > [ bonds ] > ... > A Z 1 > > That gives the following: > > | | > |-A . . . . . . . Z-| > | | > > This bond then spans the periodic boundary. > > I'm surprised the EM worked, but I am still unclear on your approach thus far. > > <snip> > >> NOTE 1 [file CNT.top, line unknown]: >> The largest charge group contains 32 atoms. >> Since atoms only see each other when the centers of geometry of the charge >> groups they belong to are within the cut-off distance, too large charge >> groups can lead to serious cut-off artifacts. >> For efficiency and accuracy, charge group should consist of a few atoms. >> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. >> > > These notes are not simply printed for your entertainment. If you have a > 32-atom charge group, you will have potentially severe artifacts, especially > if > you are using cutoff electrostatics, which you are (see additional comments > below). Please read in the manual about how to properly define charge groups. > > <snip> > >> NOTE 2 [file em.mdp, line unknown]: >> You are using a plain Coulomb cut-off, which might produce artifacts. >> You might want to consider using PME electrostatics. >> > > Again, heed the note. I cannot think of a solid reason for a modern > simulation > being conducted using cutoff electrostatics, unless the goal is to prove that > such a method is less accurate than a more modern technique like PME. Again, > these notes are your friend. I see that they return during your PR attempts. > You should not ignore the advice that grompp is giving you. The artifacts of > plain cutoffs are well-documented. > > Several other resources to consider using: > > http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > -- Blog: http://blog.4message.net -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
