Hi Amit Could you please send me your mdp file for implicit solvent remd? Many thanks
On Thu, Mar 5, 2020 at 5:07 AM Amit Kumar <amitkumar879...@gmail.com> wrote: > *Message sent from a system outside of UConn.* > > > Thank You Daniel Burns, > Actually, right now I am looking at the installation and trying to install > fresh as I found some error and created mess again while rectifying each > one. At the time of installation "mdrun_mpi -h" worked perfectly so I > thought installation is fine. But really thank you for your valuable > inputs. > > Amit Kumar > > On Wed, Mar 4, 2020 at 7:39 PM Daniel Burns <dbu...@iastate.edu> wrote: > > > Hi Amit, > > > > I’m not the best resource for solutions but I’ve been having this issue > > with gromacs 2018. It seems to be related to the process manager or our > > open mpi module we are using. The job would hang on some open mpi > > communication step. > > > > I found it would work if each replica was assigned its own entire node > but > > that becomes prohibitively resource expensive with more than a few > > replicas. > > > > I was finally able to get it to work on our least used cluster where > things > > must have been installed correctly. > > > > You might have your IT look at what’s happening with the process manager > > and open mpi or whatever dependencies you have loaded. You might try a > > small job where you can assign each replica to its own node and see if > you > > get the full output. Our IT dept has been working for two weeks and still > > haven’t gotten it to work on the other clusters. > > > > > > Dan > > > > > > On Tuesday, March 3, 2020, Amit Kumar <amitkumar879...@gmail.com> wrote: > > > > > Dear Gromacs users, > > > > > > I am trying to run a REMD simulation in gromacs 4.5.5 in implicit > solvent > > > but I am unable to get any output file containing significant data > > (logfile > > > is obtained with only developers' details) or any error file. > > > I am unable to understand why this is happening and how can I tackle > the > > > situation? > > > Kindly, help me out of this situation. > > > > > > ThankYou > > > Amit Kumar > > > > > -- > > 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.