hello everyone, i m having a peptide of 3 residue named Boc-BetaAla-Aib-OMe made from prodrg server when i give the grompp command for vacuum i.e. grompp -f boc1_vac_st.mdp -c boc1.gro -p boc1.top -o boc1_vac_st.tpr i got an error: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. i have set my rlist=0.8 and rvdw=0.7. In my gro file i m having X, Y, Z coordinates which - 1.41000 1.41000 1.41000 so i increase my X, Y, Z coordinates to - 1.65000 1.65000 1.65000 then i get no error.
tell me whether i m correct at this point. or Shd i decrease my rlist and rvdw with regards Bhawana
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