On 27 January 2013 16:23, Jason Swails <jason.swails.gmail.com> wrote:
> On Sun, Jan 27, 2013 at 6:57 AM, Thomas Evangelidis <tevang3.gmail.com
> >wrote:
>
> > Dear AMBER community,
> >
> > I have run a long simulation leaving iwrap and ntxo to their default
> values
> > (iwrap=0, ntxo=1). However, I just read in the manual that for very long
> > runs, setting iwrap = 1 may be required to keep the coordinate output
> from
> > overflowing the trajectory and restart file formats, especially if
> > trajectories are written in ASCII format instead of NetCDF. This is
> exactly
> > what happened in my case, waters and ions have diffused way too long and
> > I'm afraid that apart from performance slow down I may encounter serious
> > problems in the future as I prolong my simulation.
> >
> > Will there be any compatibility issues that are not obvious to me if I
> > switch to iwrap=1 and ntxo=2 from this point?
> >
>
> There should be no compatibility issues. I would also strongly suggest
> switching to ioutfm=1 (NetCDF trajectories), since there is almost no good
> reason not to. The ASCII trajectory will overflow as soon as the ASCII
> restart will...
>
> Note, if you switch to ntxo=2 (and ioutfm=1), you don't necessarily need
> iwrap=1.
I have two more questions:
1. Does the combination iwrap=0, ntxo=2, ioutfm=1 yield performance loss
compared with iwrap=1, ntxo=2, ioutfm=1 ?
2. In an older post Prof Case recommended avoiding the usage of NMR-based
restraints (nmropt=1) with iwrap=1. Does the same apply to ntr=1, iwrap=1,
nmropt=0? A part of my protein sticks out of the unit cell although I have
applied coordinate restraints to 20 residues (restraint_wt=200) - there's a
slight drift to the whole protein in spite of the strong coordinate
restraints.
thanks for your help,
Thomas
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Received on Sat Feb 02 2013 - 12:30:02 PST
