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

[Mishelle Oña]

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 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