Hi,
I highly recommend reading the documentation for any command you will
be using in order to understand the syntax. It may also help to do a
few of the analysis tutorials:
http://ambermd.org/tutorials/#analysis
-Dan
On Mon, Jun 13, 2016 at 12:32 PM, Angelina Malagodi
<angelinamalagodi.gmail.com> wrote:
> Can the syntax be read as is? When I tried I received this error:
>
> trajin 1 1000
>
> Error: '1': No such file or directory
>
> Error: Could not set up input trajectory '1'.
>
> On Mon, Jun 13, 2016 at 12:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> You can specify start and stop frames to the 'trajin' command, e.g. "trajin
>> 1 1000" to process only the first 1000 frames, etc.
>>
>> -Dan
>>
>> On Monday, June 13, 2016, Angelina Malagodi <angelinamalagodi.gmail.com>
>> wrote:
>>
>> > Okay, but is there a way to compare my first 10 nano seconds to say my
>> last
>> > 90ns without separating my trajectories into segments?
>> >
>> > On Mon, Jun 13, 2016 at 11:44 AM, Daniel Roe <daniel.r.roe.gmail.com
>> > <javascript:;>> wrote:
>> >
>> > > If you processed 1000 frames, the RDF that is output is calculated
>> > > from all 1000 frames.
>> > >
>> > > -Dan
>> > >
>> > > On Mon, Jun 13, 2016 at 11:38 AM, Angelina Malagodi
>> > > <angelinamalagodi.gmail.com <javascript:;>> wrote:
>> > > > To whom this may concern:
>> > > >
>> > > > I have been doing radial distribution functions using a 1000 frame
>> > > > trajectory. My results don't indicate if the results are a average
>> over
>> > > all
>> > > > of the frames or a single frame. Thank you so much!
>> > > >
>> > > > Sincerely,
>> > > >
>> > > > Angelina Malagodi
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org <javascript:;>
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > >
>> > >
>> > > --
>> > > -------------------------
>> > > Daniel R. Roe, PhD
>> > > Department of Medicinal Chemistry
>> > > University of Utah
>> > > 30 South 2000 East, Room 307
>> > > 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 <javascript:;>
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
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>> > AMBER.ambermd.org <javascript:;>
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> 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 307
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 Mon Jun 13 2016 - 12:00:04 PDT
