[gmx-users] Gromacs-fda

[Lod King]

Hi amber users
I am trying to analyze protein pairwise-forces for my protein. After
getting some files and running the following commands:

$ gmx_fda editconf -f 300.pdb -o pdb.gro
$ gmx_fda grompp -f test.mdp -c pdb.gro -p gromacs.top -o water.tpr
-maxwarn 5
$ gmx_fda make_ndx -f water.tpr

$ gmx_fda mdrun -nt 1 -rerun 1wq5_6.1.trr -pfi test.pfi -pfn index.ndx -s
water.tpr -pfa output.pfa -pfr output.pfr

I obtained index.ndx, output.pfa and out.pfr files.

In my pfr file, it shows the output with:

pairwise_forces_scalar
frame 0
0 5 3.390778e+01 48
0 4 2.046505e+00 48
0 6 -1.183681e+00 48
0 1 -1.727842e+01 112
0 2 -3.984052e+00 48
0 3 -2.990689e+00 48
0 146 4.887157e-01 48
0 148 -4.024438e-01 48
0 123 -9.690338e-01 48
0 118 -4.066894e-01 48

1. what do "48, 112" mean in my file?

2. I also attached the "test.mdp, and test.pfi" files I downloaded from the
web page, I wonder are these two files applied to all or should I be aware
of selecting them specifically?

3. during the step in generating index.ndx, I was asked to select:

0 System
  1 Protein
  2 Protein-H
  3 C-alpha
  4 Backbone
  5 MainChain
  6 MainChain+Cb
  7 MainChain+H
  8 SideChain

but after selecting 1, it generated all info including 0, 1, 2,
3....index..Do I have to make script to select only 1:protein? (index
attached too)

Three question, any answer would help..

#For .mdp

(; Run parameters
integrator    = md
nsteps          = 500000    ;
dt        = 0.002        ; 2 fs
; Output control
nstxout         = 10000        ;
nstvout         = 10000        ;
nstfout        = 0        ;
nstxtcout    = 1000        ;
;nstxout-compressed = 1000    ;
nstenergy    = 1000        ;
nstlog        = 10000        ;
; Constraints
constraint_algorithm = lincs    ;
constraints    = hbonds    ; d
lincs_iter    = 1        ;
lincs_order    = 4        ;
continuation    = yes        ;
; Neighborsearching
cutoff-scheme   = Verlet        ;
verlet-buffer-tolerance = 0.005    ;
ns_type         = grid          ;
nstlist         = 20            ;
rlist        = 1.0        ;
rcoulomb    = 1.0        ;
rvdw        = 1.0        ;
; Electrostatics
coulombtype    = PME        ;
pme_order    = 4        ;
fourierspacing    = 0.16        ;
; Temperature coupling is on
tcoupl        = V-rescale    ;
tc-grps        = System    ;
tau_t        = 0.1        ;
ref_t        = 298        ;
pcoupl        = Parrinello-Rahman    ;
pcoupltype    = isotropic    ;
tau_p        = 2.0        ;
ref_p        = 1.0        ;
compressibility = 4.5e-5    ;
pbc        = xyz        ;
DispCorr    = EnerPres    ;
gen_vel        = no
pull        = no  )

#For .psi

(onepair = summed
group1 =  Protein
group2 =  Protein
atombased = pairwise_forces_scalar
residuebased = pairwise_forces_scalar
type =  nonbonded
time_averages_period = 0)