I am sorry but my question is out of this subject.
5ns windows means dividing the simulation in steps each 5ns or not.
What is meant by this " set ig=-1 here so that the random number seed
changes automatically on every step otherwise you will get unrealistic
correlations in your results."?
Thanks
Ahmed A Ezat
On Wed, Apr 29, 2015 at 3:37 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> > On Apr 29, 2015, at 6:20 AM, anu chandra <anu80125.gmail.com> wrote:
> >
> > Dear amber users,
> >
> > I am working with membrane proteins and planing to do a microsecond long
> > simulation. I have few queries for which I would like to get your expert
> > suggestions.
> >
> > 1. I have seen from literature that many membrane protein simulations are
> > carried out with Gromacs and NAMD engine. Since I am familiar with
> Amber, I
> > wish to stick with Amber for the simulation. How safe to go with Amber
> for
> > microsecond long membrane protein simulations?
> >
>
> Perfectly fine - we regularly run multiple microsecond long simulations in
> our lipid force field development work - and likely a lot more efficient
> (if you use GPUs) than you'd get trying to do this timescale with NAMD. You
> need to decide what force field you are going to use. I would suggest
> either the AMBER lipid 14 force field (and FF14SB for the protein), which
> is very easy to use with AMBER, or the latest Charmm lipid force field,
> although in this case you will need to convert the psf file with AMBER's
> chamber or parmed programs.
>
> > 2. All my previous simulations were of 100-200ns. I ran the simulations
> > with 5 ns window and saving the trajectories every 2 ps. Here, since the
> > simulations are going to be microsecond long, How good to stick with the
> > same protocol.?. I am very much aware of the large dataset going to be
> > generated during this long run.
> >
>
> The frequency at which you write to the trajectory file is only an issue
> in terms of the amount of data you will produce. If you have plenty of disk
> space this is not an issue but you might want to consider making it less
> frequent if you don't need data every 2ps. Performance can be affected by
> writing too often but every 1000 steps+ is fine. 5ns windows is also fine,
> you might want to extend this to longer if that is easier for you to manage
> - I tend to try to shoot for 1 hour or so run time per simulation - but
> this is arbitrary and easy enough to script so just pick a time length per
> simulation that is convenient for you. Note you MUST set ig=-1 here so that
> the random number seed changes automatically on every step otherwise you
> will get unrealistic correlations in your results.
>
> I'd also suggest using the GPU code otherwise it will take you a long time
> (and tons of resources) to get to microsecond time scales.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Associate Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Associate Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Wed Apr 29 2015 - 07:00:03 PDT
