AMBER Archive (2008)

Subject: Re: AMBER: [Fwd: segmentation fault in nmode]

From: Guillaume Renvez (grenvez_at_laas.fr)
Date: Mon Jun 23 2008 - 03:27:27 CDT

I just fixed the problem as you suggested, and now the program runs
correctly.
thanks again!

   guillaume

David A. Case wrote:
> On Tue, Jun 17, 2008, Guillaume Renvez wrote:
>
>
>> I also send the input files I used, if someone else wants to try...
>> thanks!
>>
>
> The code is clearly wrong, in its initialization of the scr2() array (in
> forces.f).
>
> Try the following patch: (just commenting out three lines:)
>
> diff -c -r10.0 forces.f
> *** forces.f 15 Apr 2008 23:23:18 -0000 10.0
> --- forces.f 19 Jun 2008 23:07:31 -0000
> ***************
> *** 133,141 ****
> iptatm,scr7,scr8)
>
> lim = 3*natom*(3*natom-1)/2
> ! do jn=1,lim
> ! scr2(jn) = 0.d0
> ! end do
>
> ! subroutine pol2der(natom,x,f,p,q,h,ipair,
> ! - jpair,xrc,xij,r2,fw,vt,
> --- 133,141 ----
> iptatm,scr7,scr8)
>
> lim = 3*natom*(3*natom-1)/2
> ! !do jn=1,lim
> ! ! scr2(jn) = 0.d0
> ! !end do
>
> ! subroutine pol2der(natom,x,f,p,q,h,ipair,
> ! - jpair,xrc,xij,r2,fw,vt,
>
>
> For me, this removes the seg. fault, but I don't know if the results are
> otherwise correct.
>
> Note that your structure is not at a minimum (as least as nmode sees it), so
> you will need to make sure you get a minimum in nmode (with the same energies
> as in sander), before trusting the modes.
>
> ...hope this helps...dac
>
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