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

[Justin Lemkul]

On 10/29/15 6:21 PM, Mishelle Oña wrote:
> I attached the .mdp file I usedCould you tell me if there is a better form to

The mailing list does not accept attachments.

> calculate the free energy of my polimer?And how can I do normal convergence

I would run a much longer simulation (20 ns certainly isn't enough to sample the 
conformational ensemble of such a polymer) and look into MM/PBSA type calculations.

> checks of the dynamics?

What you analyze depends on what you're after.

-Justin

>
>> 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
>>>>>>
>>>>>> ================================================== -- Gromacs Users
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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
>>>>
>>>> ================================================== -- Gromacs Users
>>>> mailing list
>>>>
>>>> * Please search the archive at
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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
>>
>> ================================================== -- Gromacs Users mailing
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>>
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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

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