I am trying to pull the peptide through the lipid bilayer using GROMACS 4.5.6 double precision but getting the following error while carrying it out.
Program mdrun_d, VERSION 4.5.6
Source code file: pull.c, line: 329
Fatal error:
Distance of pull group 1 (5.326382 nm) is larger than 0.49 times the box size (5.435044)
What could be the probable reason for the same and how can i remove that?
Kindly help.
Regards,
Tarun
Gromacs does not automatically adjust box sizes to circumvent this problem. One must simply calculate the necessary box size (based on the length of the reaction coordinate) beforehand, and add any extra space, e.g. in the case of pressure coupling, which causes changes in the box size during the run (but usually not very large). Upgrading to a newer version will not simply fix the issue.
Your box is too small to pull over the specified distance. The COM distance between the pulled and reference groups includes periodicity. Either set up your system in a larger box to allow for pulling over this distance, or use a different pull-geometry (e.g. direction_periodic) that eliminates the influence of periodicity.
Dear Tarun Agarwa,
This is some type of specific nature so you should need to set essential parameter to the instrument and also need to change the box size too,
Whenever you try to do this you set the box as larger based on your peptide
You just check the error
Distance of pull group 1 (5.326382 nm) is larger than 0.49 times the box size (5.435044)
So that you just increase box size means this error will minimize.
The distance between pulled peptide and reference group also includes periodicity, and you should need to use some other different pull-geometry
i thing now recently some improved auto programed version was introduced so you just try to update your software from GROMACS 4.5.6 to next version, because i have seen in latest version some automatic adjustment of box size and other parameter base on sample reading info., i forget the version but via your instrument ID you just put upgrade..,
Good Luck & Regards
R.Selva............
You should change your instrumental input based on your compound requirement, because of this small box size you got this error, i agree selva chemist
Gromacs does not automatically adjust box sizes to circumvent this problem. One must simply calculate the necessary box size (based on the length of the reaction coordinate) beforehand, and add any extra space, e.g. in the case of pressure coupling, which causes changes in the box size during the run (but usually not very large). Upgrading to a newer version will not simply fix the issue.
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