[gmx-users] MPI problem------Cannot compile and link MPI code with cc

[Gavin Melaugh]

Hi guys

I have been running gromacs for a few months now with no real problems
however some of my numbers differ from my supervisor's who uses DL-POLY.
Anyway discussion of the discrpnacies has led me to questioning aspects
of my topology file below (exerpts). We created the topology ourselves.
I always thought that the set up below would calculate 1-4 interactions,
but having read through the archives I am now confused. Do I have to
give a pair list in topology file, or is gen-pairs = yes sufficient. I
never created a pairlist as I thought that gen-pairs would create it
from the parameters in atomtypes.

;Parameter level
[defaults]
; nbfunc    comb-rule     gen-pairs        fudgeLJ     fudgeQQ
     1             3                    yes                   
0.5           0.5

[atomtypes]
;type     mass           charge      ptype     sigma(nm)    
epsilon(kjmol-1)
   CB     12.011000      0.000000       A      0.355000      0.292880
   CA     12.011000     -0.115000       A      0.355000      0.292880
   HC      1.008000      0.115000       A      0.242000      0.125520
   CU     13.019000      0.265000       A      0.350000      0.334720
   NU     14.007000     -0.597000       A      0.325000      0.711280
   CH     13.019000      0.332000       A      0.385000      0.334720
   C3     15.035000      0.000000       A      0.390500      0.732200
   C2     14.027000      0.000000       A      0.390500      0.493712

;Molecular level
[moleculetype]
;       name         nrexcl
       subhexylcage      3

[atoms]
; atomnr  type   resnr  residue   name    cgnr     charge     mass
    1      CA       1    CGE       CA       1     -0.1150     12.0110
    2      CB       1    CGE       CB       1      0.0000     12.0110

[bonds]
;  ai    aj   func   b0(nm)       kb(kjmol-1 nm-2)
    1     2     1     0.1400      392459.2
    1     6     1     0.1400      392459.2

[angles]
;  ai    aj    ak   func  theta(deg)    ktheta(kjmol-1 rad-2)
    2     1     6     1     120.00      711.2800
    2     1     7     1     120.00      292.8800

[dihedrals]
;  ai    aj    ak    al    func       V1           V2            
V3            V4 (all kj mol-1)
    1     2     3     4       5       0.00000      30.33400      
0.00000       0.00000
    1     2     3    10       5       0.00000      30.33400      
0.00000       0.00000

;System level
[system]
;the name of this system
config test of 32 subhexyl cage molecules

[molecules]
; moleculename     number
 subhexylcage        32