[gmx-users] energy minimization problem

Justin Lemkul jalemkul at vt.edu
Mon Jun 1 13:46:18 CEST 2015



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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================


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