[From nobody Thu Nov 14 11:53:36 2013 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi there, thanks for that. It makes clear. Regards and ------------------------------------------------------------ Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 ------------------------------------------------------------ ________________________________________ Da: gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] per conto= di Mark Abraham [Mark.Abraham@anu.edu.au] Inviato: gioved=EC 14 ottobre 2010 3.16 A: Discussion list for GROMACS users Oggetto: Re: [gmx-users] remd with disre in gmx4.0.7 On 14/10/2010 12:09 PM, Justin A. Lemkul wrote: > > > Spitaleri Andrea wrote: >> >> ------------------------------------------------------------------------ >> <http://www.sanraffaele.org/grazieate> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ >> >> >> Hi there, >> this is a very old issue for me at lest and I still get error running >> a remd simulation using restraints for ion. I am using gmx4.0.7 >> This is my input: >> >> ; Distance restraints >> disre =3D simple >> disre_weighting =3D equal >> disre_fc =3D 1000 >> >> and in topol.top >> >> [ distance_restraints ] >> ; ai aj type index type' low up1 up2 fac >> 957 309 1 0 1 0.18 0.20 0.25 1 >> 957 338 1 1 1 0.18 0.20 0.25 1 >> 957 701 1 2 1 0.18 0.20 0.25 1 >> 957 733 1 3 1 0.18 0.20 0.25 1 >> 956 149 1 4 1 0.18 0.20 0.25 1 >> 956 185 1 5 1 0.18 0.20 0.25 1 >> 956 417 1 6 1 0.18 0.20 0.25 1 >> 956 462 1 7 1 0.18 0.20 0.25 1 >> >> So all different restraints. My input run is: >> >> #PBS -l nodes=3D120 >> mpirun mdrun_d -s remd -v -deffnm remd -multi 5 -replex 5000 -npme 8 >> -dd 4 4 1 >> >> and immediately I get: >> >> Program mdrun_d, VERSION 4.0.7 >> Source code file: disre.c, line: 143 >> >> Fatal error: >> Time or ensemble averaged or multiple pair distance restraints do not >> work (yet) with domain decomposition, use particle decomposition >> (mdrun option -pd) >> >> That's strange since I am not neither using time nor ensemble >> averages nor multiple dist restraints. > > You are using ensemble averaging, which is invoked when combining > "disre =3D simple" and mdrun -multi, per the manual. You should be able > to use mdrun -pd, as the error message suggests. That is, "disre =3D simple" and mdrun -multi combine to implement ensemble averaging. This seems not to be what the OP wanted, which seemed to be distance restraints with REMD. Other than using PD, there's no work-around in 4.0.x or current code. Mark -- 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/S= earch before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ]