[gmx-users] energy minimization problem

soumadwip ghosh soumadwipghosh at gmail.com
Mon Jun 1 08:28:34 CEST 2015


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             = full          ; Periodic Boundary Conditions (yes/no)


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


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