Thank you Professor Shirts. So now my protein itp file looks like this: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB MassB 1 CT 1 ACE CH3 1 -0.190264 12.010000 CT_per -0.120334 12.010000 .... [ bonds ] ;ai aj func th0 kb th0B kbB 1 2 1 0.10900 284512.0 0.10900 113804.8 ....
[ pairs ] 1 8 1 .... [ angles ] ;ai aj ak funct th0 kb th0B kbB 2 1 3 1 109.500 292.880 109.500 117.152 ..... [ dihedrals ] i j k l func th0 cth mult th0B cthB multB 2 1 5 6 9 180.0 2.86144 1 180.0 1.14458 1 Now, I have created 6 different lambda values and placed a well-equilibrated structure and the same topology file (with values corresp. to lambda=0 and lambda =1) within six directories. The .mdp files contain the information (init-lambda-state=0,1,..) which lambda state is it. Is my approach correct ? Secondly, when I grompp followed by gmxdump -s *.tpr I find, that there is no difference in hamiltonian between the two. So, does the scaling take place during runtime? Third, since in state B only the hamiltonian is rescaled (the perturbed entries are defined in ffnonbonded.itp file) do I need to explicitly add another section [ pairs_nb ]? Again, I thank you for replying. On Sat, Apr 20, 2013 at 5:52 PM, Michael Shirts <mrshi...@gmail.com> wrote: > You have to change atom types. For example: > > [ atomtypes ] > ;name bond_type mass charge ptype sigma epsilon > h1 h1 0.0000 0.0000 A 2.47135e-01 > 6.56888e-02 > h1_pert h1 0.0000 0.0000 A 2.47135e-01 3.56888e-02 > ; perturbed > > The mass and charge can be zero, because they will be defined in the [ > atoms ] part > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass typeB > chargeB MassB > 1 h1 1 BLAH H1a 1 -0.089 1.008 h1_pert > -0.030 1.008; perturbed > > > > On Sat, Apr 20, 2013 at 4:04 PM, HANNIBAL LECTER < > hanniballecte...@gmail.com > > wrote: > > > Hi, > > > > I am trying to perform expanded ensemble simulations between 2 states A > > (lambda=0) and B (lambda =1) with 6 intermediate lambda values. > > > > In state B the Hamiltonian is rescaled, such that the epsilons of the vdW > > interactions, the charges, the bond, angle and dihedral constants are a > > multiple of the similar terms of State A. > > > > It's not quite clear to me (going through the archives of the gmx-users > > mailing list how to perform these calculations. One way to do this, is to > > use a single topology file in which the charges and the other terms are > > specified for both states A and B. However, it is not clear as to how > > should I scale the epsilons in the topology file. (My atoms are not > mutated > > in state B. They are the same atoms with scaled epsilons.) > > > > Secondly, since I have the topology files for states A and B, is there a > > way I could perform the simulations (any particular way in grompp) where > > both the topology files can be preprocessed designating the end states > and > > using the mdp options, the simulations corresponding to the intermediate > > lambda values performed?? > > -- > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists