AMBER Archive (2005)

Subject: Re: AMBER: new tutorial available

From: Difei Wang (dwang_at_nd.edu)
Date: Fri Jan 28 2005 - 18:08:59 CST

Dear Dr. Case:

Thanks for preparing the FEP/TI tutorial.

I still have two issues regarding the calculation. I know these have not
been
discussed before. Correct me if I am wrong. I am using Amber8.

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.
Should
it be the equlibrated structure from lambda=0 or lambda=0.1127? In other
word,
after I created pert files from a PDB, what lambda value or no value should
I
use to equlibrate the system before 3 seperated sander runs?

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?

Thanks.

Difei

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, January 20, 2005 2:06 PM
Subject: AMBER: new tutorial available

> I have (finally!) assembled a tutorial on thermodynamic integration using
> sander. Follow the "Tutorials (English)" link at the Amber web site.
>
> Note that this is an "advanced" application: you will need to be familiar
with
> running other Amber simulations before attempting this one.
>
> Comments, corrections and suggestions are welcome.
>
> ...enjoy...dac
>
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