[gmx-users] Energy minimisation of solvated protein - Tutorial

Anna Duncan anna.duncan at mrc-mbu.cam.ac.uk
Fri Feb 26 13:27:40 CET 2010


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  

% 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- 

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has been replaced by 'pbc = xyz'.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...


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