[gmx-users] gro file

[Bhawana Gupta]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081111/1190ce07/attachment.html>