[gmx-users] gmx wham (again)

Justin Lemkul jalemkul at vt.edu
Sat Apr 21 03:25:28 CEST 2018 


On 4/19/18 11:25 PM, Alex wrote:
> Justin,
>
> Since that cylinder thing is buggy and I still haven't been able to 
> get a stable run (and I recall this is why I decided not to use it 
> earlier), back to the restraints...
> If the WHAM procedure produces an essential relative energy fit and 
> the radial restraints are: 1) present in every config, including bulk, 
> 2) in the direction orthogonal to the reaction coordinate, and 3) 10 
> times lower than e.g. the force constant corresponding to the ion-pore 
> binding I am after, is there much to account for in terms of 
> artifacts? This is basically a k<r^2>/2 energy term present in every 
> config, where r is perpendicular to the reaction coordinate. Anything 
> I am missing in terms of generality?
>

You're assuming that the restraint does the same amount of work in every 
window, which may not be the case.

-Justin

> Thank you,
>
> Alex
>
> On 4/19/2018 5:28 AM, Justin Lemkul wrote:
>>
>>
>> On 4/18/18 6:30 PM, Alex wrote:
>>> An otherwise perfectly well-behaved setup is doing something 
>>> catastrophic.
>>> The pull code is:
>>>
>>> ; Pull code
>>> pull                 = yes
>>> pull-coord1-type     = umbrella
>>> pull_ngroups            = 2
>>> pull_ncoords            = 1
>>> pull_group1_name        = K
>>> pull_group2_name        = CNT
>>> pull_coord1_geometry    = cylinder
>>> pull-cylinder-r         = 1.0
>>> pull-group2-pbcatom     = 1343
>>> pull_coord1_groups      = 1 2
>>> pull-coord1-vec         = 0 0 1
>>> pull_coord1_rate        = 0.0
>>> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
>>> pull_coord1_start       = yes           ; define initial COM 
>>> distance > 0
>>>
>>> Segfaults without error messages within 20-50 ps. I suspected that
>>> pull-coord1-vec is somehow hating zero coord1_rate, so I changed 
>>> that to
>>> 1.0e-9.
>>>
>>> The result is:
>>>
>>> ***
>>> Program:     gmx mdrun, version 2018
>>> Source file: src/gromacs/mdlib/sim_util.cpp (line 776)
>>> MPI rank:    0 (out of 4)
>>>
>>> Fatal error:
>>> Step 40700: The total potential energy is -nan, which is not finite. 
>>> The LJ
>>> and electrostatic contributions to the energy are 15121 and -108386,
>>> respectively. A non-finite potential energy can be caused by 
>>> overlapping
>>> interactions in bonded interactions or very large or Nan coordinate 
>>> values.
>>> Usually this is caused by a badly- or non-equilibrated initial
>>> configuration,
>>> incorrect interactions or parameters in the topology.
>>> ***
>>>
>>> No indication of exploding system at step 40000, all energies 
>>> looking legit.
>>>
>>> Any thoughts?
>>
>> Looks buggy. Can you upload a .tpr to Redmine with a description of 
>> the problem?
>>
>> -Justin
>>
>>> Alex
>>>
>>>
>>>
>>>
>>> On Wed, Apr 18, 2018 at 4:00 PM, Alex <nedomacho at gmail.com> wrote:
>>>
>>>> ... and everything is segfaulting, though worked perfectly fine 
>>>> until the
>>>> 'cylinder' thing.
>>>>
>>>> On Wed, Apr 18, 2018 at 3:45 PM, Alex <nedomacho at gmail.com> wrote:
>>>>
>>>>> Which then would be = 0 0 1, correct? This though will have to 
>>>>> coexist
>>>>> with pull_coord1_rate        = 0.0
>>>>>
>>>>> Is that reasonable?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Alex
>>>>>
>>>>> On Wed, Apr 18, 2018 at 2:11 PM, Justin Lemkul <jalemkul at vt.edu> 
>>>>> wrote:
>>>>>
>>>>>>
>>>>>> On 4/18/18 4:08 PM, Alex wrote:
>>>>>>
>>>>>>> In addition, we seem to have a different problem:
>>>>>>>
>>>>>> Cylinder geometry requires the use of pull-coord1-vec, not
>>>>>> pull-coord1-dim.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>> -------------------------------------------------------
>>>>>>> Program:     gmx grompp, version 2018
>>>>>>> Source file: src/gromacs/gmxpreprocess/readpull.cpp (line 234)
>>>>>>>
>>>>>>> Fatal error:
>>>>>>> With pull geometry cylinder the pull vector can not be 0,0,0
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Apr 18, 2018 at 6:34 AM, Justin Lemkul <jalemkul at vt.edu> 
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>> On 4/18/18 3:17 AM, Alex wrote:
>>>>>>>>
>>>>>>>> I suppose this question is mostly for Justin...
>>>>>>>>> Let me remind what I am dealing with and ask if my idea is 
>>>>>>>>> correct.
>>>>>>>>>
>>>>>>>>> I have a rectangular membrane in XY with a pore at (X/2, Y/2) 
>>>>>>>>> in water
>>>>>>>>> and want to get the Gibbs free energy curve for an ion. For 
>>>>>>>>> this, I
>>>>>>>>> have a
>>>>>>>>> bunch of starting configurations at (X/2, Y/2) and Z varying 
>>>>>>>>> between
>>>>>>>>> some
>>>>>>>>> -z0 and z0. The bias in the "fake" pull mdp is applied as N N 
>>>>>>>>> Y. Near
>>>>>>>>> the
>>>>>>>>> membrane, this means the entire plane is sampled, which adds
>>>>>>>>> contributions
>>>>>>>>> I am not interested in. I want the pore and a small region of the
>>>>>>>>> membrane
>>>>>>>>> around it, not the membrane, given its properties.
>>>>>>>>>
>>>>>>>>> So, I applied weak (k=50) in-plane restraint to the ion for 
>>>>>>>>> each of
>>>>>>>>> the
>>>>>>>>> sampled configurations -- to keep the sampling region a bit 
>>>>>>>>> closer to
>>>>>>>>> the
>>>>>>>>> pore. The results look completely different, but they finally 
>>>>>>>>> make
>>>>>>>>> very
>>>>>>>>> good qualitative sense. The ion still walks around within a small
>>>>>>>>> disk, but
>>>>>>>>> not much -- this tentatively makes me happy.
>>>>>>>>>
>>>>>>>>> Would you believe the results obtained this way, assuming 
>>>>>>>>> otherwise
>>>>>>>>> proper setup?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> This is the exact situation that the "cylinder" pull geometry is
>>>>>>>> designed
>>>>>>>> to model. I suggest going that route rather than ad hoc 
>>>>>>>> restraints,
>>>>>>>> which
>>>>>>>> will influence the PMF and should be otherwise accounted for.
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>> -- 
>>>>>>>> ==================================================
>>>>>>>>
>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>> Assistant Professor
>>>>>>>> Virginia Tech Department of Biochemistry
>>>>>>>>
>>>>>>>> 303 Engel Hall
>>>>>>>> 340 West Campus Dr.
>>>>>>>> Blacksburg, VA 24061
>>>>>>>>
>>>>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>>>>> http://www.thelemkullab.com
>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>>
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>>>>>>>>
>>>>>>>>
>>>>>> -- 
>>>>>> ==================================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Assistant Professor
>>>>>> Virginia Tech Department of Biochemistry
>>>>>>
>>>>>> 303 Engel Hall
>>>>>> 340 West Campus Dr.
>>>>>> Blacksburg, VA 24061
>>>>>>
>>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>>> http://www.thelemkullab.com
>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> -- 
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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>>>>>> or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>
>>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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

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