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