[gmx-users] File input/output error

anyone please suggest where could have I gone wrong or what can I do to rectify this error? -- Yours sincerely, Sabyasachi Sahoo Supercomputer Education & Research Center Indian Institute of Science - Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs

Re: [gmx-users] Prospective research areas of GROMACS

Thanks a lot for such in-depth insight! Will look into all of this and get started asap! On Wed, Sep 23, 2015 at 1:29 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Mon, Sep 21, 2015 at 7:10 PM Sabyasachi Sahoo <ssahoo.i...@gmail.com> > wrote:

Re: [gmx-users] Prospective research areas of GROMACS

Thanks for the suggestion! On Mon, Sep 21, 2015 at 10:58 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 21/09/15 19:09, Sabyasachi Sahoo wrote: > >> Dear Gromacs users and developers, >> >> I am a parallel programming researcher and would like to cont

[gmx-users] Prospective research areas of GROMACS

will be really appreciated. Thanks in advance. -- Yours sincerely, Sabyasachi Sahoo Supercomputer Education & Research Center Indian Institute of Science - Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List be

Re: [gmx-users] Input files for performance analysis

Thanks a lot Carsten. I am really grateful for this material. On Fri, Sep 4, 2015 at 3:04 PM, Kutzner, Carsten <ckut...@gwdg.de> wrote: > Hi, > > > On 03 Sep 2015, at 13:07, Sabyasachi Sahoo <ssahoo.i...@gmail.com> > wrote: > > > > Thank you for the paper

Re: [gmx-users] Error while using grompp

now. > > On Thu, Sep 3, 2015 at 10:59 AM, Sabyasachi Sahoo <ssahoo.i...@gmail.com> > wrote: > > > Thanks a lot! > > > > On Thu, Sep 3, 2015 at 8:13 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Hi, > > > >

[gmx-users] Error while using grompp

Dear users, I am trying to go through all the steps given in tutorial " http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Topology_preparation%2c_%22What's_in_a_log_file%22%2c_basic_performance_improvements%3a_Mark_Abraham%2c_Session_1A" and the moment I enter

Re: [gmx-users] Error while using grompp

m.mdp, as a workaround > > Mark > > On Thu, Sep 3, 2015 at 4:36 PM Sabyasachi Sahoo <ssahoo.i...@gmail.com> > wrote: > > > Dear users, > > I am trying to go through all the steps given in tutorial " > > > > > http://www.gromacs.org/Do

Re: [gmx-users] Input files for performance analysis

Thank you for the papers, but can I get access to zipped files containing input files( like .mdp and .topol or even .tpr file) that can be directly simulated. On Wed, Aug 26, 2015 at 1:16 PM, Kutzner, Carsten <ckut...@gwdg.de> wrote: > Hi, > > > On 25 Aug 2015, at 20:23

[gmx-users] Comparing various MD packages

Hello all, I am interested in comparing various MD packages like LAMMPS, GROMACS, DESMOND, NWChem, RedMD. I was looking through literature to find any relevant papers regarding the same and found a paper or two that do so. But they used different set of bench-marking problem sets, and no single

[gmx-users] Input files for performance analysis

Hello all, I have good enough experience in high performance and parallel computing and would like to find out bottlenecks in various phases of GROMACS. Can anyone please give me links to ready-to run input files of standard molecular systems to be simulated for GROMACS (to be run on

Re: [gmx-users] Building gromacs on CRAY XC40

. Roland On Tue, Jul 7, 2015 at 1:02 AM, Sabyasachi Sahoo ssahoo.i...@gmail.com wrote: Dear Gromacs users, I am trying to build gromacs on our latest supercomputer CRAY XC40, but I am unable to do so because of lack of administrator privileges and different programming environment

[gmx-users] Building gromacs on CRAY XC40

, and documentation and nothing seems to work. It be also really great if someone could give me the link to the any thread that addresses this problem. Thanx in advance. -- Yours sincerely, Sabyasachi Sahoo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support