Hi Peter, I have already created an index file with make_ndx in which I specify what atoms are in DNA1 and DNA2 groups. Moreover the two groups are present in the file topol.top. Indeed GROMACS doesn't produce any error about the declaration of them in the file .mdp. I send you also my topol.top file for clarity: .................................
; GROMACS topology ; ; Include the force field #include "/amber03.ff/forcefield.itp" ; Include chain topologies #include "topol1.itp" #include "topol2.itp" ; Include water topology #include "amber03.ff/tip4p.itp" ; Include generic ion topology #include "amber03.ff/ions.itp" [ system ] Two all-AT in water [ molecules ] DNA1 1 DNA2 1 SOL 39390 NA 190 CL 146 ............................. Thanks, Valerio 2016-01-13 20:40 GMT+01:00 Peter Stern <peter.st...@weizmann.ac.il>: > I believe that you need to define which nucleotides are in each group DNA1 > and DNA2 using make_ndx, since those are not "default" groups. I think > that you can do this and then do an Metin -rerun just to define the new > groups. > > Peter > > Sent from my iPad > > > On 13 בינו׳ 2016, at 20:53, valerio di giulio <digiuliovale...@gmail.com> > wrote: > > > > Hi, > > > > I have a problem with the use of "gmx enemat". I'm trying to calculate > > the contribution of SH-LJ to the potential that exists between two DNA > > strands with GROMACS 5.1.1. I've already got a Potential of Mean Force > > doing an umbrella sampling. > > For this reason I have already many files .edr each one linked to a > window, > > from > > which I would like to extract the SH-LJ contribution but every time I use > > "enemat" this is the output: > > > > ...................... > > > > GROMACS: gmx enemat, VERSION 5.1.1 > > Executable: /usr/local/gromacs/bin/gmx > > Data prefix: /usr/local/gromacs > > Command line: > > gmx enemat umbrella1e.edr -ljsr > > > > Opened ener.edr as single precision energy file > > Will read groupnames from inputfile > > Read 2 groups > > group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy > file > > WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file > > WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file > > WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file > > group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy > file > > WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file > > > > Will select half-matrix of energies with 0 elements > > Last energy frame read 500 time 500.000 > > Will build energy half-matrix of 2 groups, 0 elements, over 501 frames > > Segmentation fault (core dumped) > > > > ........................... > > > > Although I have written to the .mdp file: > > > > energygrps = DNA1 DNA2 > > > > Thank you in advance, > > > > Valerio Di Giulio > > -- > > 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. > -- > 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. -- 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.