Hi Johannes, it appears so:
; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_DNA_chain_E.itp" #include "topol_DNA_chain_F.itp" #include "PRB_GMX.itp" ; Include water topology #include "amber99sb-ildn.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name CRYSTAL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA in water [ molecules ] ; Compound #mols DNA_chain_E 1 DNA_chain_F 1 NA 71 CL 31 PRB 1 SOL 16349 Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, September 7, 2017 11:18:29 AM Subject: Re: [gmx-users] DPOSRES not working Dear Sergio, how did you define the position restrain in your topology? Check your topology and position restrain file. All the best Johannes On 07.09.2017 11:07, Sergio Manzetti wrote: > Hello, I am running 5 simulations with the given mdp: > > title = DNA in water stabilization > cpp = /lib/cpp > include = -I../top > define = -DPOSRES > integrator = md > dt = 0.002 > nsteps = 10000000 > nstxout = 5000 > nstvout = 5000 > nstlog = 5000 > nstenergy = 300 > nstxout-compressed = 300 > compressed-x-grps = PRB SOL NA CL DNA > energygrps = PRB SOL NA CL DNA > nstlist = 10 > ns-type = grid > rlist = 0.8 > coulombtype = PME > rcoulomb = 0.8 > rvdw = 0.8 > tcoupl = V-Rescale > tc-grps = System > tau-t = 0.1 > ref-t = 310 > Pcoupl = No > tau-p = 1.0 > compressibility = 4.5e-5 > ref-p = 1.0 > gen-vel = yes > gen-temp = 310 > gen-seed = 17527 > constraints = all-bonds > > > and still, the DNA splits into two.... > > Any ideas what could be wrong? > > Thanks > > Sergio Manzetti > > [ http://www.fjordforsk.no/logo_hr2.jpg ] > > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] > Midtun > 6894 Vangsnes > Norge > Org.nr. 911 659 654 > Tlf: +47 57695621 > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | > Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | > FAP ] > -- ______________________________________ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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.