[gmx-users] There is no error message but the dynamic don´t show the correct number of frames
Justin Lemkul
jalemkul at vt.edu
Thu Oct 29 23:11:33 CET 2015
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
>>>>
>>>> ==================================================
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>>>> Gromacs Users mailing list
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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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>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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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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