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

[Justin Lemkul]

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

==================================================