Currently I am using only gromacs16.5. As this have *"PLEASE NOTE* that the current versions do support lone pair construction on halogens, however the current construction is only compatible with GROMACS-2016.x and by using gmx grompp -maxwarn 1 to override the warning about lone pair construction."
I was unable to understand this "For all other GROMACS versions, you will have to manually edit the topology to use "3fad" construction and appropriate atom numbers."as I was using 2018.4. So I switched to version-16. But now trapped in this HtoD cudaMemcpyAsync failed: invalid argumenterror. On Tue, Aug 27, 2019 at 12:09 AM Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > You're running 2016.x which had a bug, not the 2018.x you thought you were > using. Use GMXRC or your cluster's modules to select the version you want > to use in the terminal or script that you want to use. > > Mark > > On Mon, 26 Aug 2019 at 20:34, Navneet Kumar Singh <navneet...@gmail.com> > wrote: > > > What kind of error is this. Previously Gromacs 2018.4 version was running > > fine using GPU. But Now this error I am getting. > > > > _________________________________________________________ > > > > gmx mdrun -v -deffnm em > > :-) GROMACS - gmx mdrun, 2016.5 (-: > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Herman J.C. Berendsen Par > > Bjelkmar > > Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit > Groenhof > > Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios > > Karkoulis > > Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson > > Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund > > Teemu Murtola Szilard Pall Sander Pronk Roland Schulz > > Alexey Shvetsov Michael Shirts Alfons Sijbers Peter > Tieleman > > Teemu Virolainen Christian Wennberg Maarten Wolf > > and the project leaders: > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > > Copyright (c) 2001-2017, The GROMACS development team at > > Uppsala University, Stockholm University and > > the Royal Institute of Technology, Sweden. > > check out http://www.gromacs.org for more information. > > > > GROMACS is free software; you can redistribute it and/or modify it > > under the terms of the GNU Lesser General Public License > > as published by the Free Software Foundation; either version 2.1 > > of the License, or (at your option) any later version. > > > > GROMACS: gmx mdrun, version 2016.5 > > Executable: /usr/local/gromacs/bin/gmx > > Data prefix: /usr/local/gromacs > > Working dir: /home/nitttr/Desktop/Hydroxy_chloroquine > > Command line: > > gmx mdrun -v -deffnm em > > > > > > Back Off! I just backed up em.log to ./#em.log.7# > > > > Running on 1 node with total 16 cores, 32 logical cores, 1 compatible GPU > > Hardware detected: > > CPU info: > > Vendor: Intel > > Brand: Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz > > SIMD instructions most likely to fit this hardware: AVX_512 > > SIMD instructions selected at GROMACS compile time: AVX_512 > > > > Hardware topology: Basic > > GPU info: > > Number of GPUs detected: 1 > > #0: NVIDIA Tesla P4, compute cap.: 6.1, ECC: yes, stat: compatible > > > > Reading file em.tpr, VERSION 2016.5 (single precision) > > Using 1 MPI thread > > Using 32 OpenMP threads > > > > 1 compatible GPU is present, with ID 0 > > 1 GPU auto-selected for this run. > > Mapping of GPU ID to the 1 PP rank in this node: 0 > > > > Application clocks (GPU clocks) for Tesla P4 are (3003,1531) > > > > Back Off! I just backed up em.trr to ./#em.trr.7# > > > > Back Off! I just backed up em.edr to ./#em.edr.7# > > > > Steepest Descents: > > Tolerance (Fmax) = 1.00000e+03 > > Number of steps = 50000 > > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2016.5 > > Source file: src/gromacs/gpu_utils/cudautils.cu (line 105) > > > > Fatal error: > > HtoD cudaMemcpyAsync failed: invalid argument > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > > > -- > > > > > > > > > > > > > > Thanks & Regards > > _______________________________________________________ > > > > [image: photo] > > *NAVNEET KUMAR* > > Doctoral Student > > Dept. of Pharmacoinformatics > > National Institute of Pharmaceutical Education and Research, Sector 67, > > S.A.S. Nagar - 160062, Punjab (INDIA) > > P +918017967647 <+918017967647> | > > E navneet...@gmail.com <navneet...@gmail.com> > > <http://www.linkedin.com/in/navneet-kumar-74391814a/> > > <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar> > > > > Please consider your environmental responsibility. Before printing this > > e-mail message, ask yourself whether you really need a hard copy. > > -- > > 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. > -- Thanks & Regards _______________________________________________________ [image: photo] *NAVNEET KUMAR* Doctoral Student Dept. of Pharmacoinformatics National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar - 160062, Punjab (INDIA) P +918017967647 <+918017967647> | E navneet...@gmail.com <navneet...@gmail.com> <http://www.linkedin.com/in/navneet-kumar-74391814a/> <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar> Please consider your environmental responsibility. Before printing this e-mail message, ask yourself whether you really need a hard copy. -- 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.