On Mon, 26 Jun 2017 12:25:19 +0200 Davide Bonanni <davide.bona...@unito.it> wrote:
> 1) Can I perform the calculation in a single step with soft core > potential enabled? I mean, is it correct to transform directly the > hydrogen into a chlorine instead of using 2 topologys and 2 > complexes, where in the first step I transform the hydrogen into > dummy atom, and in the second I transform the dummy atom into > chlorine. Technically speaking you can perfectly do that but in practice it can be much more efficient to directly and linearly transform one atom type into another (single topology approach). There is no need for a softcore potential in this case. Those would only be activated for atoms that either appear or disappear i.e. atoms with zero vdW parameters. The input and topology files from FEsetup should be all you need. > 2) Referring to BevanLab Tutorial 6: Free Energy Calculation ( > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm > x-tutorials/free_energy/index.html), I have to perform every step of > molecular dynamics at every Lambda value, is that right? Yes, you will need to do a simulation for every and each lambda step. > 3) I run a test minimization step (mdp file attached) of my complex > at the last "init-lambda-state", 15 in my case. Looking at the .trr > output file I can see that the bond between the carbon and the > hydrogen which should be trasformed is longer than a normal C-H bond, > but the atom is still recognized as hydrogen (picture > "http://tinypic.com/r/2wp11dh/9": purple -> init-lambda-state = 0 ; > blue -> init-lambda-state = 15). I was wondering if this is what I am > supposed to see, so if gromacs is considering the state B of my > system where I have chlorine bound to carbon instead hydrogen. What does "recognized as hydrogen" mean? I suspect that what you are referring to is the output of some visualisation program because you instructed it to interpret that particular atom to be a hydrogen. What you need to expect to see is that a C-H bond is transformed into a C-Cl bond and accordingly the bond length increases. -- 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.
