I agree with Jason all around, except for the ig=-1. I tend to set the seed
explicitly just so I can more readily reproduce the simulations. it's not
that I think ig=-1 is incorrect, I just feel more comfortable knowing that
if I run the same input I will get the same output. It does take more work.
On Fri, May 11, 2012 at 8:51 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> All are good questions.
>
> On May 11, 2012, at 3:17 AM, Dilraj LAMA <dilrajl.bii.a-star.edu.sg>
> wrote:
>
> > Dear Amber users,
> > I am currently planing to use temperature based REMD
> > for my work. For this I am learning the application following the REMD
> > tutorial mentioned in the Amber tutorial
> > http://ambermd.org/tutorials/advanced/tutorial7/.
> >
> > I have few queries and will be glad if you can kindly give me your input.
> >
> > 1) The first is regarding the chirality restraints. I am planing to
> > use the temperature range between 300-400K for my study. I have done a
> > search of the mailing list and came across threads
> > (http://archive.ambermd.org/200901/0203.html) where it was mentioned
> > that for this range of temperature, it is not critical to have the
> > chirality restraint. So I am planing to not use it for my study. Is
> > this a fair judgment?
>
> In my experience not having chirality restraints over this temperature
> range is fine.
>
> >
> > 2)In the REMD tutorial of Amber, there is an equilibration run
> > performed for all the replicas before actually doing REMD. Now in the
> > step after the equilibration, the authors have given an example of the
> > REMD.mdin (http://ambermd.org/tutorials/advanced/tutorial7/). I am
> > just appending the parameters from the input file that is bothering me
> > below.
> >
> > irest=0, ntx=1,
> > temp0=XXXXX, ig=RANDOM_NUMBER,
> >
> > REMD uses the restart file from the equilibration run. So shouldn't it
> > be that irest=1 and ntx=5 so that the velocity information is also
> > read from the restart file?
>
> When using the restart files from previous MD, use irest=1 and ntx=5 if
> and only if you wish to use the old velocities (I usually do).
>
> >
> > And why are the authors setting the random number and initial
> > temperature again for the REMD run of the tutorial when the
> > temperatures are already set in the previous equilibration run?
>
> Each replica needs its own temperature, so that value will change for each
> mdin file that controls a different replica.
>
> >
> > 3) I also have a query on the "ig" parameter. In the classical MD,
> > "ig=-1" is now routinely set in the input parameter file. Shouldn't it
> > be the case also for REMD simulations?
>
> Yes, but ig=-1 was not around when the tutorial was written. Setting ig=-1
> is the appropriate thing to do.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Fri May 11 2012 - 08:00:03 PDT
