AMBER Archive (2005)

Subject: Re: AMBER: NTWPRY problem

From: wenfei Li (wfli_at_biophy.nju.edu.cn)
Date: Mon Jul 25 2005 - 20:39:21 CDT

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Tuesday, July 26, 2005 7:54 AM
Subject: Re: AMBER: NTWPRY problem

> On Mon, Jul 25, 2005, wenfei Li wrote:
> >
> > In order to output the coordinates only for atoms 1-530 , I set the NTWPRT
> > option to 530. Before the Bugfix.all file is applied to patch the source
> > files, this option works well. However, after the latest Bugfix.all file is
> > applied, this option does not make any use, and all of the atomic
> > coordinates are printed.
>
> The change was introduced with bugfix.13, but doesn't appear to have anything
> to do with the overall purpose of that bugfix. I suspect that it is somehow
> a regression to earlier code(?).
>
> If Ross Walker is still alive, he can check bugfix.13 to see if the changes
> to corpac() calls were really intended.
>
> In the meantime, you can try the following (untested) patch; it just changes
> three lines to tell corpac() how many atoms to print out.
>
>
> Index: runmd.f
> ===================================================================
> RCS file: /thr/gamow/cvsroot/amber8/src/sander/runmd.f,v
> retrieving revision 7.260
> diff -c -r7.260 runmd.f
> *** runmd.f 2005/02/10 22:07:42 7.260
> --- runmd.f 2005/07/25 23:50:31
> ***************
> *** 1837,1843 ****
>
> if (itdump) then
> if( iwrap == 0 ) then
> ! call corpac(x,1,3*natom,12,loutfm)
> if(ntb > 0) call corpac(box,1,3,12,loutfm)
> else
> call get_stack(l_temp,3*natom)
> --- 1837,1843 ----
>
> if (itdump) then
> if( iwrap == 0 ) then
> ! call corpac(x,1,nrx,12,loutfm)
> if(ntb > 0) call corpac(box,1,3,12,loutfm)
> else
> call get_stack(l_temp,3*natom)
> ***************
> *** 1850,1856 ****
> if (ifbox == 2) call wrap_to(nspm,nsp,r_stack(l_temp),box)
> end if
> #endif
> ! call corpac(r_stack(l_temp),1,3*natom,12,loutfm)
> if(ntb > 0) call corpac(box,1,3,12,loutfm)
> call free_stack(l_temp)
> end if
> --- 1850,1856 ----
> if (ifbox == 2) call wrap_to(nspm,nsp,r_stack(l_temp),box)
> end if
> #endif
> ! call corpac(r_stack(l_temp),1,nrx,12,loutfm)
> if(ntb > 0) call corpac(box,1,3,12,loutfm)
> call free_stack(l_temp)
> end if
> ***************
> *** 1859,1865 ****
> ! Velocity archive:
>
> if (ntwv > 0) then
> ! if (mod(nstep,ntwv) == 0) call corpac(v,1,3*natom,13,loutfm)
> end if
>
> ! Energy archive:
> --- 1859,1865 ----
> ! Velocity archive:
>
> if (ntwv > 0) then
> ! if (mod(nstep,ntwv) == 0) call corpac(v,1,nrx,13,loutfm)
> end if
>
> ! Energy archive:
>
>
> ....thanks for the report.....good luck....dac
>
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