[gmx-users] Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750)
aacharya at iitk.ac.in
Sat May 4 09:40:33 CEST 2013
It seems you are following the pull code parameters from Justin's
tutorial. First thing first, i would look at the box size requirements for
my protein of interest and set the box size accordingly and not use the
size provided in the tutorial.
Now, assuming you are just trying to run the tutorial first, you have made
one mistake in specifying the parameters. The pull_dim parameter should be
N N Y and not Y Y Y. Giving Y Y Y means that you are telling the algorithm
to pull the protein in all three directions. Now the direction of pull in
any direction should not exceed 0.49 of the box length in the particular
direction. That is what the error is all about.
So if you need to pull in all three directions by a particular distance,
then make sure that the box length in all directions are greater than
twice the pull distance.
Structural and Computational Biology Lab
> I am studying protein-ligand interaction through umbrella sampling. I used
> the following value foe md_pull.mdp file
> pull = umbrella
> pull_geometry = distance ; simple distance increase
> pull_dim = Y Y Y
> pull_start = yes ; define initial COM distance > 0
> pull_ngroups = 1
> pull_group0 = Protein
> pull_group1 = prc
> pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_k1 = 1000 ; kJ mol^-1 nm^-2
> and box size details is
> editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
> 6.560 4.362 12
> while runnimg the command for
> mdrun -s pull.tpr
> Have the following error
> "Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the
> box size (2.184750)"
> I request you to kindly help me to debug the error
> Thanking You with Regards.
> Arunima Shilpi
> Ph. D Research Scholar(Cancer & Epigenetics)
> Department of Life Science
> National Institute of Technology
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