[gmx-users] gro file

[Mark Abraham]

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          
> 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.

Mark