[gmx-users] gmx wham (again)

Alex nedomacho at gmail.com
Fri Apr 20 05:25:51 CEST 2018 

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?

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
>>>>>>>
>>>>>>> ==================================================
>>>>>>>
>>>>>>> -- 
>>>>>>> Gromacs Users mailing list
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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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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>
>

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