[gmx-users] Fwd: problem in energy minimization

[neelam wafa]

Thanks sir Mark,

I have compared the complex before and after the minimization. there are
slight differences in the bond angles and interactions. overall posture is
not much different.
Previously I had run a simulation with same problem but the rmsd output was
stable. Are these results reliable?

Looking forward for your valuable suggestions.

Regards


On Wed, Jul 18, 2018 at 5:42 PM, neelam wafa <neelam.wafa at gmail.com> wrote:

> Thanks sir Mark,
>
> I have compared the complex before and after the minimization. there are
> slight differences in the bond angles and interactions. overall posture is
> not much different. I have attached  a picture of the pymol session
> comparing the two . blue one is after minimization. please have a look on
> it.
> Previously I had run a simulation with same problem but the rmsd output
> was stable.
>
> Looking forward for your valuable suggestions.
>
> Regards
>
> Neelam
>
> On Wed, Jul 18, 2018 at 9:47 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> That could be fine, as your potential energy is large and negative. We
>> can't tell from the outside. Do visualise the before and after to get some
>> clues.
>>
>> Mark
>>
>> On Tue, Jul 17, 2018, 19:11 neelam wafa <neelam.wafa at gmail.com> wrote:
>>
>> > ---------- Forwarded message ----------
>> > From: neelam wafa <neelam.wafa at gmail.com>
>> > Date: Tue, Jul 17, 2018 at 1:12 PM
>> > Subject: problem in energy minimization
>> > To: gromacs.org_gmx-users at maillist.sys.kth.se
>> >
>> >
>> > Hi,
>> >
>> > Dear gromacs users, I am running md simmulation of a protein with a
>> ligand.
>> > i have already done it with the same protein and a different ligand. Now
>> > when i run em md run i get following result.
>> >
>> > Energy minimization has stopped, but the forces have not converged to
>> the
>> > requested precision Fmax < 1000 (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.
>> > You might need to increase your constraint accuracy, or turn
>> > off constraints altogether (set constraints = none in mdp file)
>> >
>> > writing lowest energy coordinates.
>> >
>> > Steepest Descents converged to machine precision in 150 steps,
>> > but did not reach the requested Fmax < 1000.
>> > Potential Energy  = -9.3659806e+05
>> > Maximum force     =  1.0269271e+04 on atom 4399
>> > Norm of force     =  9.8929054e+01
>> >
>> > NOTE: 10 % of the run time was spent in pair search,
>> >       you might want to increase nstlist (this has no effect on
>> accuracy)
>> >  please guide me is it reliable to proceede for simmulation. or there is
>> > something wrong. Is it a sign of system instability?
>> >
>> > looking forward for your cooperation.
>> >
>> > Regards
>> > --
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