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

[Toan Nguyen]

How would we go about doing another energy minimization? I realized I sent
the wrong tutorial earlier, I was actually following this one Absolute
Binding Free Energy - Gromacs 2016
<http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016>
by David Mobley.

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 procedure.
>
> -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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