[gmx-users] CNT Grompp errors and Force Field modifications

[Christopher Stiles]

Ok I am trying to use the GROMOS96 43a1 force field to run a simulation of a
finite CNT. I believe I have figured out how this force field can be
modified. I have made the following additions to the respective 43a1 force
field files and placed them in the root directory of the simulation:

 

#####################################

*******************

ffG43a1bon.itp

*******************

#define gb_48     0.142100  4.7890e+06

; C     -   C

 

#define ga_47       120.00      397.48

; C      - C     - C

 

*******************

ffG43a1.rtp

*******************

[ UNK ]

 [ atoms ]

  

 [ bonds ]

     C     C   gb_48

 [ angles ]

    C     C     C     ga_47

 [ impropers ]

    C     C     C     0     ga_1

 

*******************

ffG43a1.n2t

*******************

C         C         1          C
; CNT Carbon with one bond

C         C         2          C         C                                 :
CNT double bonded Carbon

#####################################

 

Note I also made the following change to ffG43a1bon.itp (the original line
was):

#define gd_1    180.000       5.86          2

; -C-C- 1.4

Now it is:

#define gd_1    167.360       5.86          2

; -C-C- 1.4

 

I still get the following errors when I run grompp(here is the first 10):

*****************************************************

WARNING 1 [file "SWNT_6_6_144.top", line 167]:

  No default Bond types, using zeroes

WARNING 2 [file "SWNT_6_6_144.top", line 167]:

  No default Bond types for perturbed atoms, using normal values

WARNING 3 [file "SWNT_6_6_144.top", line 168]:

  No default Bond types, using zeroes

WARNING 4 [file "SWNT_6_6_144.top", line 168]:

  No default Bond types for perturbed atoms, using normal values

WARNING 5 [file "SWNT_6_6_144.top", line 169]:

  No default Bond types, using zeroes

WARNING 6 [file "SWNT_6_6_144.top", line 169]:

  No default Bond types for perturbed atoms, using normal values

WARNING 7 [file "SWNT_6_6_144.top", line 170]:

  No default Bond types, using zeroes

WARNING 8 [file "SWNT_6_6_144.top", line 170]:

  No default Bond types for perturbed atoms, using normal values

WARNING 9 [file "SWNT_6_6_144.top", line 171]:

  No default Bond types, using zeroes

WARNING 10 [file "SWNT_6_6_144.top", line 171]:

  No default Bond types for perturbed atoms, using normal values

*****************************************************

 

At http://cs86.com/CNSE/CNT_FFOpt0.zip a zip file with all the files I use
can be obtained, and the grompp command I use is:

 

grompp -f md_200k.mdp -c SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top -maxwarn
10 -pp

 

Also note I am working off the modifications I made to the Gromacs FF and
they are as follows:

 

*****************************************************

ffgmx.n2t and add the following 2 lines:

 

C C 1 C ; CNT Carbon with one bond

C C 2 C C ; CNT double bonded Carbon

 

 

ffgmxbon.itp

 

add the following line to it:

*** To be very clear about this the first two lines are just telling what
section to add it to in the file and what the units of that addition
reprsent.***

 

#####################################

[ bondtypes ]

; i j func b0 kb

C C 1 0.14210 478900.

#####################################

[ angletypes ]

; i j k func th0 cth

C C C 1 120.000 397.480

#####################################

[ dihedraltypes ]

; i l func q0 cq

C C 1 0.000 167.360

#####################################

*****************************************************

 

Thank you very much for your help!

 

~Christopher Stiles 
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA

 

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