[gmx-users] CNT is apparently broken during energy minimization step
Justin Lemkul
jalemkul at vt.edu
Fri Aug 14 15:02:08 CEST 2015
On 8/14/15 8:58 AM, Victor Rosas Garcia wrote:
> 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.
>
I think this is just a side effect of uploading a partial file (to the OP: bad
practice to do this, as it's just confusing, so either share a file or don't
rather than trying to post what you think might be relevant). Your point
stands, though, as there are clearly missing or incorrect bonded interactions
that distort the CNT. The simplest check is to look at a few atoms that get
clearly separated and check the parameters associated with them and their neighbors.
-Justin
> 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.
>>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
More information about the gromacs.org_gmx-users
mailing list