Hi,
I have the same problem as listed below back in February. I am using
the latest gromacs version (4.0.7) and tried the solution below by
entering
genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro
instead of making the output as pdb file. Yet the same result occurs
with the same error message. One of the box lengths is smaller than
twice the cut-off length.
Please let me know what other options I can try.
Thanks!
nayef
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original message below
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Hi Anna,
You should mention the version of Gromacs you're using. One of the
versions did not write the box correctly to pdb files, which I think
happened in your case. If you take as the solvation step
genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro
instead of writing output to 1qlz-water.pdb, I think you should be fine.
The reason for writing a .pdb file is the easier visualization with a
multitude of programs.
Thanks for your interest in the tutorial.
Cheers,
Tsjerk
On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan
<anna.duncan at mrc-mbu.cam.ac.uk> wrote:
Hi,
I've been trying to go through the 'Introduction to Molecular Dynamics
Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the
tutorials listed on the GROMACS website.
I've got to the stage where I am performing energy minimisation on my
solvated protein but when I use grompp to create the .tpr file for mdrun, I
get the error message:
One of the box lengths is smaller than twice the cut-off length. Increase
the box size or decrease rlist
I am using the protein with pdb ID 1QLZ, one of the suggested structures for
the tutorial and have so far carried out the following commands:
% pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh
% grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr
% mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb
% editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0
% genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb
% grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr
% genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname
NA+ -nname CL-
% grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o
1qlz-EM-solvated.tpr
after which I receive the error message.
The minim_pbd.mdp file I use in the last grompp command is the same as
minim.mdp used in previous grompp commands (the latter file I downloaded as
part of the tutorial) except that the line 'pbc = no' has been replaced by
'pbc = xyz'.
I have tried increasing the value of 'd' in the editconf command, to 2,3 and
even 8 but this doesn't make any difference. (I have read that it is not a
good idea to tamper with the cut-off values so have avoided doing that) The
box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0 in
mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong...
Anna
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--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
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