AMBER Archive (2004)

Subject: Re: AMBER: increasing the maximum value of NPHB parameter

From: Alena Shmygelska (oshmygel_at_cs.ubc.ca)
Date: Thu Dec 02 2004 - 01:42:44 CST

Hello Amber Users,

Thanks Dr. David Case for answering my questions and giving me pointers, I
found where else one should modify the size of arrays if one wants to
increase the maximum NPHB value allowed in Amber 7 (apart from modifying
sizes of ASOL and BSOL arrays in parms.h):
in box.h two arrays are declared of size of NPHB:
RADHB - the optimal interaction distance for h-bond
WELHB - the maximum well depth of h-bond interaction

Cheers,
Alena

University of British Columbia
Vancouver, BC, Canada

On Tue, 30 Nov 2004, David A. Case wrote:

> On Mon, Nov 29, 2004, Alena Shmygelska wrote:
>>
>> I have the following problem, I'd like to increase the maximum value in
>> Amber 7 for:
>> NPHB from 200 -> to 3600 (affects ASOL, BSOL, HBCUT 200 -> 3600)
>
>> Using a debugger I found that IX(I02) and IX(I14) do not refer to the
>> valid memory locations, IX array is declared of size I79.
>
> The IX array should actually have "lasti" elements; as far as I can tell,
> "I79" is not used in the code. But from your debugging, please try to figure
> out what the values of I02 and I14 are before the call to fastwt(), then
> maybe you can back-track to where there were set (in locmem), and see
> someplace where they are being overwritten (if that is indeed the case).
>
> Be sure to add -DHAS_10_12 to your MACHINE file if you have not already done
> so -- otherwise, all 10-12 interactions are assumed to vanish. (The program
> should be checking for this, but I haven't looked at Amber 7 in a while.)
>
> ....dac
>
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