Hi Daniel
Thanks but there are problems.
1) Though in manual 'pairwise' expects ref <filename> so I use something
like this (and other commands like 'nastruct' works fine in this way)
reference initial.inpcrd
pairwise :1,154 out pairwise.out eout e.out ref initial.inpcrd
But it gives error Error: [pairwise] Not all arguments handled:
[initial.inpcrd ]
It works fine if you comment it <filename> out like this:
reference initial.inpcrd
pairwise :1,154 out pairwise.out eout e.out ref ####initial.inpcrd
2) I get eout output as:
PAIRWISE: Frame 0
PAIRWISE: Cumulative Evdw: Evdw < -1.0000, Evdw > 1.0000
PAIRWISE: Cumulative Eelec: Eelec < -1.0000, Eelec > 1.0000
PAIRWISE: Frame 1
PAIRWISE: Cumulative Evdw: Evdw < -1.0000, Evdw > 1.0000
PAIRWISE: Cumulative Eelec: Eelec < -1.0000, Eelec > 1.0000
PAIRWISE: Frame 2
PAIRWISE: Cumulative Evdw: Evdw < -1.0000, Evdw > 1.0000
PAIRWISE: Cumulative Eelec: Eelec < -1.0000, Eelec > 1.0000
so on....
I tried to set cuteelec and cutevdw to 0 but no delta values are printed.
Whats wrong with my input I am not getting.
On Thu, May 15, 2014 at 7:15 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I just realized that some documentation is missing for the 'pairwise'
> command. To get individual atom energies and deltas you need to
> specify 'eout <filename>'. Note this will only report deltas greater
> than the cutoffs given by 'cuteelec' and 'cutevdw'.
>
> Hope this helps,
>
> -Dan
>
> On Thu, May 15, 2014 at 11:25 AM, newamber list <newamberlist.gmail.com>
> wrote:
> > Hi All
> >
> > I am using pairwise option as follows. It does not give me any different
> > results if I use reference or not.
> >
> > trajin md.nc
> > reference initial.inpcrd
> > pairwise :1,154 out pairwise.out ref initial.inpcrd
> >
> >
> > To check this I should get zero EELEC and EVDW (which should be delta) if
> > calculated on initial structure itself but I dont get zero values
> >
> > trajin initial.inpcrd
> > reference initial.inpcrd
> > pairwise :1,154 out pairwise.out ref initial.inpcrd
> >
> >
> > Am I doing it wrong way?
> >
> > Thanks for any suggestions
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu May 15 2014 - 12:30:04 PDT
