[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

maria goranovic mariagoranovic at gmail.com
Thu Jan 20 11:03:25 CET 2011


I have a protein whose topology I built using pdb2gmx with the -ss option
and the opls-aa force field. When I run grompp, the total charge on the
protein is reported as 2.9 (not 2.999). Why a non-zero charge? Does this
have something to do with the disulfide bridge?

Secondly, when I run a simulation of the same protein (7000 atoms) with
certain restraints in vacuum, the simulation runs very slow. I am wondering
why. I am not using particle decomposition. the box size is 50 x 50 x 50 nm.
Using 4.5.3

Maria G.
Technical University of Denmark
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