I attached the .mdp file I usedCould you tell me if there is a better form to calculate the free energy of my polimer?And how can I do normal convergence checks of the dynamics? ThanksMishelle
> To: gmx-us...@gromacs.org > From: jalem...@vt.edu > Date: Thu, 29 Oct 2015 18:11:20 -0400 > Subject: Re: [gmx-users] There is no error message but the dynamic don´t show > the correct number of frames > > > > On 10/29/15 6:08 PM, Mishelle Oña wrote: > > Well, I am trying to calculate the Solvation free energy of my molecule, I > > am following the Hands-on tutorial > > Solvation free energy of ethanol of Sander Pronk. Using trjconv I cut one > > frame from this trajectory and make all the steps of the tutorial. When I > > do g_bar to calculate the free energy there was an error:WARNING: Some of > > these results violate the Second Law > > of Thermodynamics: > > > > This is > > can be the result of severe undersampling, or (more likely) > > > > there > > is something wrong with the simulations. > > I am not sure why this error come from. Could you tell me if I should redo > > the dynamic? or what is the most suitable answer for this error. > > I doubt you'll be able to get a properly converged answer for a polymer of > that > size with these free energy methods. Without seeing a full .mdp file, > there's > not much to go on. You should also do normal convergence checks of the > dynamics. > > -Justin > > > Thanks a lotMishelle > > > >> To: gmx-us...@gromacs.org > >> From: jalem...@vt.edu > >> Date: Thu, 29 Oct 2015 17:48:59 -0400 > >> Subject: Re: [gmx-users] There is no error message but the dynamic don´t > >> show the correct number of frames > >> > >> > >> > >> On 10/29/15 5:46 PM, Mishelle Oña wrote: > >>> Hi Justin, Thanks for your reply. I used gmxcheck to verify the > >>> trajectory and it didn´t have errors. I got this: > >>> Item #frames Timestep (ps)Step 40001 0.5Time > >>> 40001 0.5Lambda 40001 0.5Coords 40001 0.5Velocities > >>> 40001 0.5Forces 0Box 40001 0.5 > >>> I am not sure if the "Forces" item is correct or not. > >>> Could you tell me why it is 0 ? > >> > >> You have nstfout = 0 in your .mdp file. Only the data you request are > >> saved. > >> > >> -Justin > >> > >>> Thanks Mishelle > >>>> To: gmx-us...@gromacs.org > >>>> From: jalem...@vt.edu > >>>> Date: Thu, 29 Oct 2015 16:52:57 -0400 > >>>> Subject: Re: [gmx-users] There is no error message but the dynamic don´t > >>>> show the correct number of frames > >>>> > >>>> > >>>> > >>>> On 10/29/15 4:50 PM, Mishelle Oña wrote: > >>>>> > >>>>> Hi!I am simulating a polimer of Polylactic acid with 30 monomers in a > >>>>> water > >>>>> system. For equilibrate the system I have made NVT, NPT and Process > >>>>> dynamics. > >>>>> The fiinal dynamic should have 40 000 frames but when I load it in VMD > >>>>> it has > >>>>> only 12 186 frames. Also the confout.gro file that result from the > >>>>> dynamic > >>>> > >>>> VMD probably ran out of memory. What it thinks is there doesn't > >>>> necessarily > >>>> reflect reality. Use gmxcheck on the trajectory to verify its contents. > >>>> Then > >>>> try stripping out waters with trjconv and loading that in VMD. > >>>> > >>>> -Justin > >>>> > >>>>> shows the polimer out of the box. I tried to center the polimer. At the > >>>>> end > >>>>> of the simultation this message appeared: Reading file topol.tpr, > >>>>> VERSION > >>>>> 4.5.5 (single precision) > >>>>> > >>>>> Starting 32 threads > >>>>> > >>>>> Making 3D domain decomposition 8 x 2 x 2 > >>>>> > >>>>> > >>>>> > >>>>> WARNING: This run will generate roughly 8233 Mb of data > >>>>> > >>>>> > >>>>> > >>>>> starting mdrun 'UNITED ATOM STRUCTURE FOR MOLECULE 3M9 in water' > >>>>> > >>>>> 10000000 steps, 20000.0 ps. > >>>>> > >>>>> > >>>>> > >>>>> NOTE: Turning on dynamic load balancing > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> Writing final coordinates. > >>>>> > >>>>> > >>>>> > >>>>> Average load imbalance: 7.6 % > >>>>> > >>>>> Part of the total run time spent waiting due to load imbalance: 1.7 % > >>>>> > >>>>> Steps where the load balancing was limited by -rdd, -rcon and/or -dds: > >>>>> X 5 % > >>>>> Y 9 % Z 14 % > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> Parallel run - timing based on wallclock. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> NODE (s) Real (s) (%) > >>>>> > >>>>> > >>>>> Time: 9229.145 9229.145 100.0 > >>>>> > >>>>> > >>>>> 2h33:49 > >>>>> > >>>>> > >>>>> (Mnbf/s) (GFlops) (ns/day) (hour/ns) > >>>>> > >>>>> Performance: 1786.838 66.381 187.233 0.128 > >>>>> > >>>>> > >>>>> > >>>>> gcq#247: "Let's Unzip And Let's Unfold" (Red Hot Chili Peppers) > >>>>> > >>>>> I don´t know if there is any error in the dynamic > >>>>> > >>>>> Then I opened the md.log file and in some steps there was this line:DD > >>>>> load > >>>>> balancing is limited by minimum cell size in dimension X YDD step > >>>>> 9998749 > >>>>> vol min/aver 0.625! load imb.: force 6.3% Please could anyone help me > >>>>> with > >>>>> an idea of what is happening? The previous simulation (NPT) doesn´t > >>>>> have this > >>>>> messages. Thanks a lot Mishelle > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>> > >>>> -- > >>>> ================================================== > >>>> > >>>> 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. > > > > > > -- > ================================================== > > 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.
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