You can do them separately, but the charges need to have been turned off for the molecule you are transforming for the second step when turning off vdw. In other words, all charges must be 0.0 for the molecule in the topology file for the vdw transformation. Is that what you've done?
Justin's tutorial gives an explanation on why this needs to be done, and in his topology he had all charges at 0.0 in the methane topology file. Okey, one thing that I presumed while performing the second transformation is that it is sufficient to 'turn-off' charge electrostatics just by stating c-lambda0=none and c-lambda1 = vdw (or vice-versa). It doesn't matter if the topology files have the charges or not. Therefore, i had included the charges in my topology file. Then this explains the problem in my case. Thank you so much Wes for clarifying that out. Sincerely, Abhishek Acharya -- 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.
