I am preparing a system of a protein with 60 molecules of cosolute molecule in aqueous medium.............
This is a WARNING..........how can I sort out? In 'md.mdp' file 'rlist value is 1.00......
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
Please go through the following links:
http://www.gromacs.org/Documentation/Errors?highlight=force#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
https://www.researchgate.net/post/Can_anyone_explain_me_about_The_sum_of_the_two_largest_charge_group_radii_is_larger_than_rlist
https://www.researchgate.net/post/How_can_i_set_up_correct_gromacs_mdp_file_options_for_cut-off
An alternative way to generate the simulation set up is to use charmm gui.
I would say that your charges in your cosolute topology might need a second look. Seems like your charge groups seems a bit off.
Gromos53A6 are based on charge groups and, in principle, one charge group should yield a net charge of 0. Also, if your partial charges are too high (in absolute terms), even though their sum = 0, you might need a larger rlist.
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