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

[Mishelle Oña]

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.
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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