Hi Mark, Thanks for the reply. I have attempted to run this on Gromacs installed on a local machine as well as on a cluster. In either case, the simulations would not complete after being run for ~12 hours. I feel that there is an error in my mdp file but I am not sure what it could be.
I'm trying to minimize the structure with a net charge of +8 in vacuum and then conduct simulated annealing in vacuum to determine the low energy gas-phase equilibrium structures to compare with collisional activation studies by ion mobility spectrometry. Thanks again for taking time to help me out. Sincerely, Tarick On Thu, Jun 16, 2016 at 4:08 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > We can't help if all we have is the information "does not produce an > output." I suggest doing tutorial material locally before you get involved > with the complexity of a cluster. > > Mark > > On Thu, 16 Jun 2016 19:01 Tarick E <telba...@gmail.com> wrote: > > > I have tried a number of edits to my minim.mdp file for minimization with > > no luck. I can generate a tpr without any errors and initiate a > simulation > > via mdrun, but no matter what resources I allocate to it (on a > > supercomputer), I cannot produce an output. > > > > Here's my mdp file. I am trying to minimize the structure that I will > then > > feed into an md simulation in vacuum: > > > > ; minim.mdp - used as input into grompp to generate em.tpr > > integrator = steep ; Algorithm (steep = steepest descent > > minimization) > > emtol = 1000.0 ; Stop minimization when the maximum > force > > < 1000.0 kJ/mol/nm > > emstep = 0.001 ; Energy step size > > nsteps = 50000 ; Maximum number of (minimization) steps > to > > perform > > > > ; Parameters describing how to find the neighbors of each atom and how to > > calculate the interactions > > nstlist = 1 ; Frequency to update the neighbor > list > > and long range forces > > rlist = 0 > > cutoff-scheme = group > > ns_type = grid ; Method to determine neighbor > list > > (simple, grid) > > coulombtype = cut-off ; Treat all long-range > > electrostatics > > rcoulomb = 0 ; Short-range electrostatic cut-off > > rvdw = 0 ; Short-range Van der Waals cut-off > > pbc = no ; Periodic Boundary Conditions > > (yes/no) > > > > > > Any help is greatly appreciated! > > > > On Wed, Jun 15, 2016 at 4:50 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 6/15/16 4:46 PM, Tarick E wrote: > > > > > >> Thanks for the help! > > >> > > >> I am following the Lysozyme tutorial except I am not solvating with > > water > > >> or balancing the charge with counter ions. When generating my .tpr > with > > >> grompp, I am receiving the error: > > >> > > >> ERROR 1 [file minim_nick_edit1.mdp]: > > >> With Verlet lists only full pbc or pbc=xy with walls is supported > > >> > > >> > > > Then you need cutoff-scheme = group. > > > > > > -Justin > > > > > > > > > I have removed periodic boundary conditions. See my mdp below for a > > simple > > >> minimization: > > >> > > >> title = Energy Minimization ; Title of run > > >> > > >> ; The following line tell the program the standard locations where to > > find > > >> certain files > > >> cpp = /lib/cpp ; Preprocessor > > >> > > >> ; Define can be used to control processes > > >> define = -DFLEXIBLE > > >> > > >> ; Parameters describing what to do, when to stop and what to save > > >> integrator = cg ; Algorithm (cg = conjugate gradient, > > >> steep > > >> = steepest descent minimization) > > >> emtol = 10.0 ; Stop minimization when the maximum > > force > > >> < 1.0 kJ/mol > > >> nstcgsteep = 10 ; ; Frequency of steepest > > descents > > >> steps when doing CG > > >> nsteps = 5000 ; Maximum number of (minimization) > steps > > >> to > > >> perform > > >> nstenergy = 1 ; Write energies to disk every > nstenergy > > >> steps > > >> energygrps = System ; Which energy group(s) to write to > disk > > >> > > >> ; Parameters describing how to find the neighbors of each atom and how > > to > > >> calculate the interactions > > >> nstlist = 0 ; Frequency to update the neighbor > list > > >> ns_type = simple ; Method to determine neighbor list > > >> (simple, grid) > > >> rlist = 0 > > >> coulombtype = cut-off ; Treatment of long range electrostatic > > >> interactions > > >> epsilon_rf = 78 > > >> rcoulomb = 0 ; long range electrostatic cut-off > > >> rvdw = 0 ; long range Van der Waals cut-off > > >> constraints = none ; Bond types to replace by constraints > > >> pbc = no ; Periodic Boundary Conditions > (yes/no) > > >> > > >> > > >> On Tue, Jun 14, 2016 at 1:07 PM, Justin Lemkul <jalem...@vt.edu> > wrote: > > >> > > >> > > >>> > > >>> On 6/14/16 1:02 PM, Tarick E wrote: > > >>> > > >>> Hey everyone, > > >>>> > > >>>> I am new to this, so please forgive me if this has been asked > before. > > >>>> > > >>>> I am trying to conduct an energy minimization in vacuum on > individual > > >>>> proteins and small peptides at a constant temperature, but I am > having > > >>>> > > >>>> > > >>> There is no temperature during energy minimization. > > >>> > > >>> trouble with this. Is there any documentation someone can lead me to > > for > > >>> > > >>>> producing a vacuum-phase minimization .mdp file? I have been trying > to > > >>>> edit > > >>>> the various .mdp files provided in the Lysozyme tutorial written by > > >>>> Justin > > >>>> Lemkul, but I haven't had any luck and I can't seem to locate any > info > > >>>> in > > >>>> the Gromacs users manual. > > >>>> > > >>>> > > >>>> Set all cutoffs to zero and do not use PBC. Then you're in vacuum. > > >>> > > >>> -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. > > >>> > > >>> > > > -- > > > ================================================== > > > > > > 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. > > > > > -- > > 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? 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