[gmx-users] GROMOS96 parameters in itp file obtained from PRODRG

[sulatha M. S]

Dear gromas users,

I am new to gromacs and trying to run polyacrylate MD simulation. I obtained
an itp file using PRODRG (gromos 96 force-field parameters). When I compare
with the same forcefield parameters in the gromacs/top directory, they are
far too off. For eg.


[ bonds ]
; ai  aj  fu    c0, c1, ...
   2   1   2    0.125  13400000.0    0.125  13400000.0 ;   CAC  OAD
   2   3   2    0.125  13400000.0    0.125  13400000.0 ;   CAC  OAE
   4   2   2    0.153   7150000.0    0.153   7150000.0 ;   CAB  CAC
   4   5   2    0.153   7150000.0    0.153   7150000.0 ;   CAB  CAA
   4   6   2    0.153   7150000.0    0.153   7150000.0 ;   CAB  CAG
   7   6   2    0.153   7150000.0    0.153   7150000.0 ;   CAH  CAG
   7   8   2    0.153   7150000.0    0.153   7150000.0 ;   CAH  CAI




As I understand, the function type should be 1 and c1 values should
correspond to the force constant for bond stretching. But here it
corresponds to the pair wise non bond parameters as listed in the
gromacs/top force-field file. Similarly,



[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   5   1                                           ;   OAD  CAA
   1   6   1                                           ;   OAD  CAG
   2   7   1                                           ;   CAC  CAH
   3   5   1                                           ;   OAE  CAA
   3   6   1                                           ;   OAE  CAG
   4   8   1                                           ;   CAB  CAI
   4  11   1                                           ;   CAB  CAL
   5   7   1                                           ;   CAA  CAH
 there are no pair terms listed here in the pairs section.


[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   2    126.0       770.0    126.0       770.0 ;   OAD  CAC  OAE

   1   2   4   2    117.0       635.0    117.0       635.0 ;   OAD  CAC  CAB

   3   2   4   2    117.0       635.0    117.0       635.0 ;   OAE  CAC  CAB

   2   4   5   2    109.5       520.0    109.5       520.0 ;   CAC  CAB  CAA

   2   4   6   2    109.5       520.0    109.5       520.0 ;   CAC  CAB  CAG

   5   4   6   2    109.5       520.0    109.5       520.0 ;   CAA  CAB  CAG

   4   6   7   2    109.5       520.0    109.5       520.0 ;   CAB  CAG  CAH

For angles also the fu term is 2 instead of 1, although the angle and the
force constant parameters are correct.

Similar errors are there in the dihedrals section also.



This means I need to almost fully edit the itp file I got from PRODRG to
proceed further. Thank you in advance for any help and please clarify
whether the itp file from PRODRG is unreliable even while using GROMOS96
force field ?



Thanking you,



Dr. M. S Sulatha

Women Scientist

Chemical Engineering Dept.

IIT-Madras, Chennai

India
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