AMBER Archive (2006)Subject: RE: AMBER: Question about Streptavidin/Biotin Tutorial.

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Sep 18 2006 - 17:10:39 CDT

Dear Shu,

> I ran the Streptavidin/Biotin tutorial. In md0.in the system
> was warmed from 0 to 300. But md1.in starting with the final
> velocity from md0.in also warmed from 0 to 300. I don't
> understand the seting of md1.in. It means system has high
> velocity at 0 degree. Is there anyone who can help me out?

cold start belly equil
&cntrl
IREST = 0, ibelly= 1,
NTX = 1, TEMPI = 0.0,
NTB = 0,
NTT = 1, TEMP0 = 298.0, TAUTP = .1,
DTEMP = 2.0, NTP = 0,
NSTLIM= 1000, DT = .002,
NTC = 2,
NTF = 2,
SCEE = 1.2,
CUT =999.0, NSNB = 9999,
NTPR = 20, NTWX = 20,
&end
&ewald
eedmeth=5,
&end
-- belly = residues 15A from BTN res 479 plus all H2O
RES 5 17
....

Here the calculation is not a restart (irest=0) and so there are no initial
value of tempi which here is 0.0 hence no initial velocities are assigned
and the system is heated up from 0K. When we move to md1.in the following is
present:

cold start belly equil
&cntrl
IREST = 1, ibelly= 1,
NTX = 5, TEMPI = 0.0,
NTB = 0, NRUN = 1,
NTT = 1, TEMP0 = 298.0, TAUTP = .1,
DTEMP = 2.0, NTP = 0,
NSTLIM= 2000, DT = .002,
NTC = 2,
NTF = 2,
IDIEL = 0, SCEE = 1.2,
CUT =999.0, NSNB = 9999,
NTPR = 20, NTWX = 20,
&end

Here irest=1 which means the calculation is a restart and that the initial
velocities are to be read from the restart file. In this situation any
setting of tempi is ignored. The initial temperature of this restart run
should thus be the same as the final temperature from the first run.

Note: this tutorial is very out of date and should not be relied on for
advice on how to run current simulations. The calculation still uses belly
to do restraints and is doing a gas phase simulation (not recommended even
in the best of cases). It also makes use of carnal which was defunct as of
Amber 7.0. You should ideally stick with the first 5 or so tutorials listed
on the Amber website - those on the Amber workshop, the psc workshop page,
DNA, MM-PBSA, Loop Dynamics and NMR refinement.

An update of all of the tutorials is currently underway and it is likely
that many of the out of date ones (such as the Streptavidin tutorial) will
shortly be removed and replaced with new tutorials.

All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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