I am trying to perform a simulation regarding the effect that hydration has on tensile response for my system. When i looked into the umbrella sampling tutorial it said to create a start file using the
pdb2gmx -f input.pdb -ignh -ter -o complex.gro command and was wondering what effect that the -ignh option had on my simulated results? do the hydrogens not get accounted for in this simulation, and if so, how are the atomic bonds in which the hydrogens are supposed to be located treated in terms of replacing those hydrogens? does this mean i am doing a united atom model ? *"The simplicity of nature is not to be measured by that of our conceptions. Infinitely varied in its effects, nature is simple only in its causes, and its economy consists in producing a great number of phenomena, often very complicated, by means of a small number of general laws."* *--Pierre Simon de Laplace* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
