[gmx-users] There is no error message but the dynamic don´t show the correct number of frames
Mishelle Oña
samimishu at hotmail.com
Fri Oct 30 00:03:27 CET 2015
I am looking for the energy of solvation. The g_mmpbsa tool could help me for it ?
> To: gmx-users at gromacs.org
> From: jalemkul at vt.edu
> Date: Thu, 29 Oct 2015 18:38:58 -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 6:21 PM, Mishelle Oña wrote:
> > I attached the .mdp file I usedCould you tell me if there is a better form to
>
> The mailing list does not accept attachments.
>
> > calculate the free energy of my polimer?And how can I do normal convergence
>
> I would run a much longer simulation (20 ns certainly isn't enough to sample the
> conformational ensemble of such a polymer) and look into MM/PBSA type calculations.
>
> > checks of the dynamics?
>
> What you analyze depends on what you're after.
>
> -Justin
>
> >
> >> To: gmx-users at gromacs.org From: jalemkul at 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-users at gromacs.org From: jalemkul at 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-users at gromacs.org From: jalemkul at 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
> >>>>>>
> >>>>>> jalemkul at 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-request at 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
> >>>>
> >>>> jalemkul at 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-request at 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
> >>
> >> jalemkul at 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-request at 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
>
> jalemkul at 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-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list