AMBER Archive (2004)

Subject: Re: AMBER: regular ewald sum in Amber8

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 24 2004 - 14:12:30 CDT

On Fri, Sep 24, 2004, Jianwen Jiang wrote:

> I am a new comer to Amber, and trying to test the regular ewald
> calculations in Amber8.
>
> According to the Amber8 manual, I simply set ew_type = 1 and ran sander.
> The program ended up with:
>
> Exceeding lastrst in get_stack
> lastrst = 1566538
> top_stk= 1433106
> isize = 477702
> request= 1910808
> Increase lastrst in the &cntrl namelist
>
> I checked the manual, but could not find the keyword "lastrst". Were
> there any other keywords required to be added into the input file? In
> addition to set ew_type=1, should I also set use_pme=0?

The "lastrst" variable is not supposed to need to be set by users in Amber 8,
but this probably doesn't apply if you are using the regular Ewald code.

You will have to modify sander.f to get enough stack memory. Look
for the lines:

      allocate( r_stack(1:lastrst), stat = ier )
      REQUIRE( ier == 0 )

and right before this, set lastrst to the value you will need for your
example.

...good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu