Hi,
I've just noticed that there are two bugs in this command. The first
causes it to look for a data set name before looking for a reference
structure. If you change your input to something like:
pairwise P0 :1,154 out pairwise.out eout e.out ref initial.inpcrd
it won't complain. However, the second bug is more serious, and
prevents the delta E calculation from ever succeeding. This will be
addressed in an upcoming bugfix but until then you can only use
pairwise to get total non-bonded energies.
Thanks for the report,
-Dan
On Thu, May 15, 2014 at 1:14 PM, newamber list <newamberlist.gmail.com> wrote:
> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> 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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Received on Thu May 15 2014 - 14:30:02 PDT
