[gmx-users] gmx wham (again)
Justin Lemkul
jalemkul at vt.edu
Thu Apr 19 13:28:33 CEST 2018
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
>>>>>>
>>>>>> * 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
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 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
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> 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
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 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
==================================================
More information about the gromacs.org_gmx-users
mailing list