Hi Justin I downloaded the compressed folder from this website: http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Computing_potentials_of_mean_force%3A_Justin_Lemkul,_Session_2A
Within it the the npt_umbrella.mdp file reads continuation = yes, gen-vel = yes. I've ran ~15 simulations over the weekend with continuation = yes, gen-vel= no Are these simulations unsuitable for umbrella sampling? --------------------------- I am assuming they are, so I've started a new sequence with not_umbrella.mdp reading the same as: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp This produces this error: WARNING 1 [file npt_umbrella.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. Since I am not equilibrating I've avoided this using the -maxwarn command and started a new sequence for umbrella sampling. ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Saturday, November 22, 2014 1:29 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella Sampling gromacs 5.0 error On 11/21/14 7:26 AM, Justin Lemkul wrote: > > > On 11/20/14 7:52 PM, Alexander Law wrote: >> Hi Justin >> >> Thank you for taking the time and helping me out. I am now using the 4.6.5 >> version to avoid this sort of error, however I have come across another error >> which I am not too sure about, it is at the start of the umbrella sampling >> section of your tutorial, after allocating which frames are to analysed >> during >> umbrella sampling. The error reads: >> >> ERROR 1 [file npt_umbrella.mdp]: >> Generating velocities is inconsistent with attempting to continue a >> previous run. Choose only one of gen-vel = yes and continuation = yes. >> >> This is after the command: grompp -f npt_umbrella.mdp -c conf1.gro -p >> topol.top -n index.ndx -o npt1.tpr >> >> I am assuming that it is better to delete the continuation command and let >> the >> pull coding take place, as I have not changed the amount of force being >> applied in the Z axis and therefore should be identical to the previous >> simulation (at frame 1, at frame 100, the chain will be shifted). But I am >> unsure which one should be omitted. >> > > The "continuation" keyword indicates whether or not constraints have already > been solved, which they have in this case, but it's really irrelevant. The > easiest thing to do is just set gen_vel = yes to start a new run. I thought I > had corrected this long ago, but apparently not. > The file provided in the tutorial should not trigger this error; it has "continuation = no" and "gen_vel = yes," which is consistent with starting a new run. I don't know how the error could have been triggered unless you have modified the file. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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. This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information. -- 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.