Have anybody been constructing virtual sites for calculating PMF via FEP?
2013/4/6 Yuri Garmay <[email protected]> > Hi all! > > I have a problem. So as it can be seen in the theme I am trying to improve > sampling of free energy calculating simulation by using replica exchange. > In the gmx4.6 it is simple while using FEP technique, but does not > implemented for umbrella sampling. But I want evaluate potential of mean > force between two flexible molecules, so I have decided to do this with > FEP+REMD. > > It is desirable to select distance between the mass centres as a reaction > coordinate, but FEP has to do with bonds or constraints between single > atoms. Luckily there virtual sites are possible to define in gromacs. So I > have a thought of using it. > > But I have never been using virtual sites and so have some questions. > I introduced two virtual sites in topology with these lines: > > -------------------- > *.top: > [ atomtypes ] > ;name mass charge ptype sigma epsilon > DD 0.0 0.0 V 0 0 ; nb interaction off? > > [ implicit_genborn_params ] > ; Atomtype sar st pi gbr hct > DD 0.0 0 0.0 0.0 0.0 ; interaction with solvent off? > > [ atoms ] > .......some lines ..... > 111 DD 9 DDD DD 111 0 > 112 DD 10 DDD DD 112 0 > > [ virtual_sitesn ] > ; Site from funct a d > 111 2 1 2 ... ; virtual site at mass centre of some groupe > 112 2 82 83 ... > > [ bonds ] > .... > 111 112 6 0.3 1000 1.3 > 1000 ; harmonic bond > .... > > *.gro: > 9DDD DD 111 0.000 0.000 0.000 /// position have to be > determined automatically? > 10DDD DD 112 0.000 0.000 0.000 > ------------------ > > The energy minimization showed correct constraint length at first sight. > But does this method solve problem I have? I will be very much appreciated > if someone experienced explains me whether this is correct or there are > pitfalls at this way. > > > -- > Best regards, > Yuri > > -- Best regards, Yuri -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
