[gmx-users] gro file
Mark.Abraham at anu.edu.au
Tue Nov 11 06:19:55 CET 2008
Bhawana Gupta wrote:
> 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
> then i get no error.
So your cutoff is now consistent with your box size.
> tell me whether i m correct at this point.
> or Shd i decrease my rlist and rvdw
There've been posts on this in the last week or two. rvdw and rcoulomb
should not be varied much (or at all) from whatever they were when the
force field was parameterized, otherwise your physics is garbage. At the
moment your .tpr describes a numerical procedure that is well-enough
formed to give to mdrun. Whether it will explode or produce a useful
result depends on all the other decisions you've made.
Since you haven't said what you're trying to do with this peptide, we
really can't assess whether you're "correct". It's also not our job to
do so... We didn't get our knowledge and judgement magically, we got it
from doing lots of reading and experimentation. You'll learn better if
you do likewise.
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