Dear Mark and Vitaly,
In order to get help, here I describe the more detailed procedure.
I successfully generated the gro and top files using pdb2gmx.
pdb2gmx -f -o -p -ter
And also the grompp finished successfully.
grompp -f -c -p -o
Then I ran the mdrun in parallel way, only to find that the polymer became
many pieces.
mpirun -np 4 mpimdrun -s -o -c -e -g -v
Obviously, it cannot form any bonds between those pieces due to the long
distances.
With the same tpr file,I ran the mdrun in non-parallel-way, however, the
polymer seems to behave properly.
mdrun -s -o -c -e -g -v
The partial files (gro, top, and mdp) are given as follows:
gro file:
Great Red Owns Many ACres of Sand
1382
1DIA N1 1 -0.199 0.069 0.078
......
125AMI H42 1382 -0.073 -0.681 -1.613
3.61500 4.27230 2.77190
top file:
......
[ molecules ]
; Compounds #moles
Protein_D 1
mdp file:
......
define = -DFLEXIBLE
constraint = none
integrator = steep
nsteps = 10000
ns_type = grid
nstcgsteep = 100
nslist = 10
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
DispCorr = EnerPres
fourierspacing = 0.36
pme_order = 4
ewald_rtol = 1e-5
emtol = 10
emstep = 0.01
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