[gmx-users] CNT is apparently broken during energy minimization step
Victor Rosas Garcia
rosas.victor at gmail.com
Fri Aug 14 14:58:32 CEST 2015
Hello Soumadwip,
from a quick look, it seems to me that your topology is missing many bonds.
The bonds section specifies atom numbers like "1 403", but I don't see
bonds with atom numbers ranging in the 100's or the 200's. In addition, I
don't see any bond angles defined. I saw distortions similar to these
while working with long-chain lipids, and my topologies were missing bond
angle definitions.
Hope this helps
Victor
2015-08-14 7:11 GMT-05:00 soumadwip ghosh <soumadwipghosh at gmail.com>:
> Hi,
> I am simulating a 5X5 carbon nanotube in the presence of nucleic acids
> in Tip3P water. I have made this nanotube using VMD nanotube builder and
> made the topology using pdb2gmx. Upto the energy minimization step every
> thing was fine but when I proceed for energy minimization I get the carbon
> naotube crumpled when I view the em.gro file in VMD. It is worth mentioning
> that the nucleic acid remains unchanged during the em process and when I am
> going for NVT equilibration it does not produce any LINCS warning or stuffs
> like that. So is it happening because a visualization tool is unaware of
> the molecular topology or do I need to change some parameters in the em.mdp
> file?
>
> The cnt.itp file is as follows (partwise)
>
> ; File 'cnt.top' was generated
> ; By user: onbekend (0)
> ; On host: onbekend
> ; At date: Sat May 30 11:07:23 2015
> ;
> ; This is a standalone topology file
> ;
> ; It was generated using program:
> ; pdb2gmx_d - VERSION 4.5.6
> ;
> ; Command line was:
> ; pdb2gmx_d -f nishCNT.pdb -o init.gro -p cnt.top
> ;
> ; Force field was read from current directory or a relative path -
> path addeed
>
>
> [ moleculetype ]
> ; Name nrexcl
> SDG 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB
> chargeB massB
> ; residue 0 SDG rtp SDG q 0.0
> 1 CA 0 SDG C1 1 0 12.011 ;
> qtot 0
> 2 CA 0 SDG C2 2 0 12.011 ;
> qtot 0
> 3 CA 0 SDG C3 3 0 12.011 ;
> qtot 0
> 4 CA 0 SDG C4 4 0 12.011 ;
> qtot 0
> 5 CA 0 SDG C5 5 0 12.011 ;
> qtot 0
> 6 CA 0 SDG C6 6 0 12.011 ;
> qtot 0
> 7 CA 0 SDG C7 7 0 12.011 ;
> qtot 0
> 8 CA 0 SDG C8 8 0 12.011 ;
> qtot 0
> 9 CA 0 SDG C9 9 0 12.011 ;
> qtot 0
> 10 CA 0 SDG C10 10 0 12.011 ;
> qtot 0
> 11 CA 0 SDG C11 11 0 12.011 ;
> qtot 0
> 12 CA 0 SDG C12 12 0 12.011 ;
> qtot 0
> 13 CA 0 SDG C13 13 0 12.011 ;
> qtot 0
> 14 CA 0 SDG C14 14 0 12.011 ;
> qtot 0
> 15 CA 0 SDG C15 15 0 12.011 ;
> qtot 0
> 16 CA 0 SDG C16 16 0 12.011 ;
> qtot 0
> 17 CA 0 SDG C17 17 0 12.011 ;
> qtot 0
>
> [ bonds ]
> ; ai aj funct b0 kb
> 1 2 1 C6 H3 0.108 284512.0
> 1 6 1 C5 H4 0.108 284512.0
> 1 403 1 0.108 284512.0
> 2 3 1 C4 C7 0.1375 255224.0
> 2 385 1 C370 C386 0.1375 255224.0
> 3 4 1 C5 C10 0.1375 255224.0
> 3 7 1 C8 C369 0.1375 255224.0
> 4 5 1 C6 C400 0.1375 255224.0
> 5 400 1 C383 C399 0.1375 255224.0
> 6 404 1 0.108 284512.0
> 7 8 1 C9 C11 0.1375 255224.0
> 8 9 1 C10 C14 0.1375 255224.0
> 8 11 1 C12 C353 0.1375 255224.0
> 9 10 1 C4 C384 0.1375 255224.0
> 9 14 1 C13 C368 0.1375 255224.0
> 11 12 1 C13 C15 0.1375 255224.0
> 11 353 1 C338 C354 0.1375 255224.0
> 12 13 1 C14 C18 0.1375 255224.0
> 12 15 1 C16 C337 0.1375 255224.0
> 13 18 1 C17 C352 0.1375 255224.0
> 14 368 1 C351 C367 0.1375 255224.0
> 15 16 1 C17 C19 0.1375 255224.0
> 15 337 1 C322 C338 0.1375 255224.0
> [ angles ]
> ; ai aj ak funct th0 cth ubo
> cub
> 2 1 6 5 120.00 334.72 0.24162
> 29288.0
> 2 1 403 5 120.00 251.04 0.21525
> 18409.6
> 6 1 403 5 120.00 251.04 0.21525
> 18409.6
> 1 2 3 5 120.00 334.72 0.24162
> 29288.0
> 1 2 385 5 120.00 334.72 0.24162
> 29288.0
> 3 2 385 5 120.00 334.72 0.24162
> 29288.0
> 2 3 4 5 120.00 334.72 0.24162
> 29288.0
> 2 3 7 5 120.00 334.72 0.24162
> 29288.0
> 4 3 7 5 120.00 334.72 0.24162
> 29288.0
> 3 4 5 5 120.00 334.72 0.24162
> 29288.0
> 4 5 400 5 120.00 334.72 0.24162
> 29288.0
> 1 6 404 5 120.00 251.04 0.21525
> 18409.6
> 3 7 8 5 120.00 334.72 0.24162
> 29288.0
> 7 8 9 5 120.00 334.72 0.24162
> 29288.0
> 7 8 11 5 120.00 334.72 0.24162
> 29288.0
> 9 8 11 5 120.00 334.72 0.24162
> 29288.0
> 8 9 10 5 120.00 334.72 0.24162
> 29288.0
> 8 9 14 5 120.00 334.72 0.24162
> 29288.0
> 10 9 14 5 120.00 334.72 0.24162
> 29288.0
> 8 11 12 5 120.00 334.72 0.24162
> 29288.0
> 8 11 353 5 120.00 334.72 0.24162
> 29288.0
> 12 11 353 5 120.00 334.72 0.24162
> 29288.0
>
> [ dihedrals ]
> ; ai aj ak al funct phi0 cp mult
> 6 1 2 3 9 180.00 12.9704 2
> 6 1 2 385 9 180.00 12.9704 2
> 403 1 2 3 9 180.00 12.9704 2
> 403 1 2 385 9 180.00 12.9704 2
> 2 1 6 404 9 180.00 17.5728 2
> 403 1 6 404 9 180.00 10.0416 2
> 1 2 3 4 9 180.00 12.9704 2
> 1 2 3 7 9 180.00 12.9704 2
> 385 2 3 4 9 180.00 12.9704 2
> 385 2 3 7 9 180.00 12.9704 2
> 1 2 385 386 9 180.00 12.9704 2
> 3 2 385 386 9 180.00 12.9704 2
> 2 3 4 5 9 180.00 12.9704 2
> 7 3 4 5 9 180.00 12.9704 2
> 2 3 7 8 9 180.00 12.9704 2
> 4 3 7 8 9 180.00 12.9704 2
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_cnt.itp"
> #endif
>
> My energy minimization.mdp file is as follows
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent
> minimization)
> emtol = 1000.0 ; Stop minimization when the maximum force
> < 1000.0 kJ/mol/nm
> emstep = 0.001 ; Energy step size
> nsteps = 5000 ; Maximum number of (minimization) steps to
> perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and
> long range forces
> ns_type = grid ; Method to determine neighbor list
> (simple, grid)
> rlist = 1.0 ; Cut-off for making neighbor list (short
> range forces)
> coulombtype = PME ; Treatment of long range electrostatic
> interactions
> rcoulomb = 1.0 ; Short-range electrostatic cut-off
> rvdw = 1.0 ; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>
> Here is how the CNT molecule looks like after energy minimization.
> https://drive.google.com/open?id=0B7SBnQ5YXQSLOUQwUFBnY3dGMnM
>
> Last but not the least I am absolutely sure that my nano tube is
> appropriately capped with hydrogen atoms. Every files are getting generated
> and the equilibrations are also happening without any difficulty but the
> CNT apparently is crumpled when visualized in VMD. what should I do?
> I appreciate your help
>
> Soumadwip
> Research Fellow
> IITB
> India
> --
> 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-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list