[gmx-users] Problems with Energy Minimization in Solvated Ligand

[Toan Nguyen]

Is it okay to see this same warning when running npt and nvt?

"*WARNING: Listed nonbonded interaction between particles 1 and 119*
*at distance 2.103 which is larger than the table limit 2.000 nm.*

*This is likely either a 1,4 interaction, or a listed interaction inside*
*a smaller molecule you are decoupling during a free energy calculation.*
*Since interactions at distances beyond the table cannot be computed,*
*they are skipped until they are inside the table limit again. You will*
*only see this message once, even if it occurs for several interactions.*

*IMPORTANT: This should not happen in a stable simulation, so there is*
*probably something wrong with your system. Only change the table-extension*
*distance in the mdp file if you are really sure that is the reason."*

On Thu, Dec 28, 2017 at 6:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/28/17 9:36 PM, Toan Nguyen wrote:
>
>> How would we go about doing another energy minimization? I realized I sent
>>
>
> Double precision, or using conjugate gradients, or using steepest descents
> with a smaller initial step.
>
> the wrong tutorial earlier, I was actually following this one Absolute
>> Binding Free Energy - Gromacs 2016
>> <http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energ
>> y_-_Gromacs_2016>
>> by David Mobley.
>>
>
> Good luck getting that to converge with a peptide :)
>
> -Justin
>
>
> On Thu, Dec 28, 2017 at 6:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 12/28/17 8:40 PM, Toan Nguyen wrote:
>>>
>>> Hi,
>>>>
>>>> I am currently following the Gromacs Tutorial by Bevan Lab (Link
>>>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm
>>>> x-tutorials/complex/05_EM.html>)
>>>> to run a simulation on a ligand from the 1mnb protein. However, I am
>>>> running into issues with the energy minimization step where I run *gmx
>>>> mdrun -v -nt 1 -deffnm em*, but an error arises saying,
>>>>
>>>> *"WARNING: Listed nonbonded interaction between particles 1 and 119*
>>>> *at distance 2.108 which is larger than the table limit 2.000 nm.*
>>>>
>>>> *This is likely either a 1,4 interaction, or a listed interaction
>>>> inside*
>>>> *a smaller molecule you are decoupling during a free energy
>>>> calculation.*
>>>> *Since interactions at distances beyond the table cannot be computed,*
>>>> *they are skipped until they are inside the table limit again. You will*
>>>> *only see this message once, even if it occurs for several
>>>> interactions.*
>>>>
>>>> *IMPORTANT: This should not happen in a stable simulation, so there is*
>>>> *probably something wrong with your system. Only change the
>>>> table-extension*
>>>> *distance in the mdp file if you are really sure that is the reason."*
>>>>
>>>> and then energy minimization runs for ~120 steps before saying,
>>>>
>>>> *"Energy minimization has stopped, but the forces have not converged to
>>>> the*
>>>> *requested precision Fmax < 100 (which may not be possible for your
>>>> system).*
>>>> *It stopped because the algorithm tried to make a new step whose size
>>>> was
>>>> too*
>>>> *small, or there was no change in the energy since last step. Either
>>>> way,
>>>> we*
>>>> *regard the minimization as converged to within the available machine*
>>>> *precision, given your starting configuration and EM parameters.*
>>>>
>>>> *Double precision normally gives you higher accuracy, but this is often
>>>> not*
>>>> *needed for preparing to run molecular dynamics.*
>>>>
>>>> *writing lowest energy coordinates.*
>>>>
>>>> *Steepest Descents converged to machine precision in 94 steps,*
>>>> *but did not reach the requested Fmax < 100.*
>>>> *Potential Energy  = -1.4016720e+05*
>>>> *Maximum force     =  1.9569155e+03 on atom 259*
>>>> *Norm of force     =  9.6724640e+01"*
>>>>
>>>> When I do the tutorial with the provided input files, this message does
>>>> not
>>>> show up and the energy minimization reaches 500+ steps. How can I fix my
>>>> input files so that the energy minimization does not run into the
>>>> problem
>>>> above?
>>>>
>>>> Below is the link to my input files:
>>>> Link
>>>> <https://drive.google.com/drive/folders/1a38C0lnBWi6n1IfalGU
>>>> -SKc0_cnxBRqa?usp=sharing>
>>>>
>>>> The messages above just indicate you probably have a bad contact
>>> somewhere
>>> early on in the minimization process. If EM finishes (which it does),
>>> then
>>> the bad contact has been at least somewhat resolved. The forces are still
>>> somewhat high, so you will likely need additional minimization and/or
>>> double precision, as the message from mdrun suggests.
>>>
>>> The protein-ligand complex tutorial isn't really relevant here; you just
>>> have a very simple protein in water, not that it makes much difference.
>>> But
>>> don't get too hung up on having a "ligand" in your system. You have a
>>> peptide, so it's nothing that requires any really special procedur
>>> <https://maps.google.com/?q=that+requires+any+really+special+procedur&entry=gmail&source=g>
>>> e.
>>>
>>> -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.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==================================================
>>>
>>> --
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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.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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