Thanks so much for your answer Prof Simmerling.
I did consider repeating the simulation with different glycan starting conformations but wasn't sure of how to proceed.
They were added using the online Glycam server and their fit subsequently optimized by rotating the N-linked glycosidic linkages' chi, psi and phi torsion angles until no protein-glycan or glycan-glycan clashes were found. The final angles were kept close to the literature values for the most populated N-linked Asn conformations.
To explore the effect of model building in a repeat simulation would I need to choose a different rotamer at the core mannose branch point of the complex glycan? If so, it would probably be three simulations having either tg, gg or gt rotamers and torsion-adjusted to remove clashes.
Would these simulations have to be repeated by seeding new productions at 10 and 20ns as I described in my previous post? Or can a single long simulation from different glycan conformations provide enough evidence of reproducibility?
Regards
Lizelle
________________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: 20 October 2017 02:08:22 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Independent production runs
I would say that this depends very much on what you are trying to learn,
and what information you have to start.
Different properties converge at different rates, so the length of the MD
should ideally be several times longer than the timescale of the properties
you are investigating. Also, if any part of your initial structure is a
model, you will want/need to show that the results do not depend on how you
built that model. For example, if you added part of the structure
(glycans?) you'll want to add them in a different conformation and make
sure that any conclusions drawn from the simulation are not strongly
dependent on how you made your initial model. Simply repeating the
simulation from the same model will not explore that sensitivity, since it
will just tell you that the results are the same if you start with the same
model.
hope that helps .. there is not really 1 simple answer.
On Fri, Oct 20, 2017 at 7:28 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
wrote:
> Hi All,
>
> I am aiming towards 30ns of production dynamics and have been advised to
> repeat this 3 times to demonstrate data reproducibility but am not sure how.
> As suggested in the manual, I've used ig=-1 throughout heating,
> equilibration and production - is this correct?
>
> Here's the input file for the first section of production, restarting from
> equilibration.rst7 and reading its velocities.
>
> First Dynamic Simulation with Constant Pressure
>
> # Control section
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 5,
> ntb = 2, ntp = 1, pres0 = 1.0, taup = 1.0,
> cut = 10.0,
> ntc = 2, ntf = 2,
> temp0 = 300.0,
> ntt = 3, gamma_ln = 2, ig = -1,
> nstlim = 500000, dt = 0.002,
> ntwx = 5000, ntpr = 5000, ntwe = 5000, ntwr = -100000,
> ioutfm = 1,
> iwrap = 1,
> ntr = 0,
> ntwprt = 0,
> nmropt = 1,
> /
> &wt type = 'END'/
> DISANG = NDOM_rnb.RST
> /
>
> There's a wall-clock time-limit on our HPC so the simulations were
> restarted each time using the input given above until the desired
> trajectory length was reached (always irest=1, ntx=5 and ig=-1).
>
> I don't really understand the concept of MD reproducibility very well...
> Could someone please explain this to me?
>
> Currently, I can think of two ways for restarting the production but don't
> know which is correct:
> 1. using ig=-1, irest=0, ntx=1 and starting from the same initial
> equilibrated coordinates as used for the first production
> 2. using ig=-1, irest=0, ntx=1 but starting from the rst7 file saved at
> 10ns for the second and 20ns for the third repeat production
>
> Would option two demonstrate data reproducibility or just explore more
> conformational space (or are they the same thing)?
> Is something like 30ns generally acceptable thesedays to investigate the
> motion of glycans and protein breathing or should it be increased?
>
> Kind regards
>
> Lizelle Lubbe
>
> PhD (Medical biochemistry) candidate
> Department of Integrative Biomedical Sciences
> University of Cape Town
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