On 01/20/11, maria goranovic <mariagorano...@gmail.com> wrote: > Hi > > 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? > >
Something is materially wrong, like mangled termini. Have a look at the resulting structure. > 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 > > Have a look at the end of the .log file for some performance data. How are you assessing "very slow"? Mark
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