AMBER Archive (2005)

Subject: Re: AMBER: new tutorial available

From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 28 2005 - 18:57:28 CST

On Fri, Jan 28, 2005, Difei Wang wrote:
>
> 1.For charge calculation in water, you set lambda=0.1127, 0.5, 0.8873 for 3
> MD calculations. From the perl script, I realized for lambda=0.5, it started
> from the rst file from lambda=0.1127; and for lambda=0.8873, it read rst
> file of lambda=0.5. But what is the input coordinate file for lambda=0.1127.

You do need an equilibrated starting point. Since the lambda=0.1127 step has
its own equilibration in the perl script, it should not matter whether you
equilibrate before that at lambda=0 or lambda=0.1127.

Please remember that the tutorial explains one way to do things, and is not
intended as a cookbook recipe. If you are concerned about whether the
equilibration procedure makes a difference, or whether I have sampled long
enough, or at enough lambda points (etc.), please run your own tests and see
what happens.

>
> 2.When I set nstlim =100000, ntave=5000, I expect to have an AVERAGE SUMMARY
> at every 5000 steps. It did report at every NSTEP=5000 but the line is "A V
> E R A G E S O V E R 2500 S T E P S". When I set nstlim =100000,
> ntave=10000, the line is "A V E R A G E S O V E R 5000 S T E P S". After
> I checked the source code runmd.f, I realized this value is called nvalid
> and equals ntave/nrespa. Because I set nrespa=2, So it reported at every
> ntave/2 steps, am I right?

Yes, you are right. The total energy is available only every nrespa steps,
and so the number of points in the averages is reduced by that amount.

...dac

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