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

[Mishelle Oña]

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 ?
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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