On 6/1/15 2:28 AM, soumadwip ghosh wrote:
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
Please upload an image somewhere and provide the URL.
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?
Possibly; see below.
The cnt.itp file is as follows (partwise)
Incomplete topologies are not generally useful.
; 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 = full ; Periodic Boundary Conditions (yes/no)
If this is part of your work using the CHARMM force field, these nonbonded
settings are incorrect. The effect on minimization is probably not significant,
but you shouldn't get in the habit of using wrong settings. It probably
wouldn't explain any sort of severe geometry distortion, though.
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?
Hard to say without seeing what "crumpled" means, but likely you should not just
be pushing ahead. If the CNT is indeed deforming badly, that suggests something
is wrong with the topology and any simulation you do will be junk.
-Justin
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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