[gmx-users] There is no error message but the dynamic don´t show the correct number of frames

Mishelle Oña samimishu at hotmail.com
Thu Oct 29 23:21:56 CET 2015 

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-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
> >>>>
> >>>> ==================================================
> >>>> --
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> >>>    		 	   		
> >>>
> >>
> >> --
> >> ==================================================
> >>
> >> 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
> >>
> >> ==================================================
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> >> Gromacs Users mailing list
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> >   		 	   		
> >
> 
> -- 
> ==================================================
> 
> 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
> 
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