Dear expert, I have created topology for an unstudied (simulation) molecule, and I can run it successfully.
1- How many or which quantities at least must be checked with experiment to become sure of the created topology? and if we find some difference with experiment, to what percent this differences can be acceptable? (for instance, if the experimental value of the density is 920 kg/m^3, is 1000 kg/m^3 OK?). 2- If we intend to improve the differences with the experimental values, what are the best ways? is changing slightly the charges on the atoms can be a good way (let us say we correctly have defined bonds, angels, ect according to the force filed)? Thank you in advance, Best regards -- 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 gmx-users-requ...@gromacs.org.
