Dear Amberusers,
The Reason for the Temperature Drop was answered by Hannes Loeffler, it
was due to the fact that ntx=7 was used and it was a NetCDF-File,
changeing to ntx=5 solved the problem.
>
> On Wed, 3 May 2017 09:16:49 +0200
> Johannes Kalliauer <johannes.kalliauer.tuwien.ac.at> wrote:
>
> > What is the difference between:
> > ntx=5 and ntx=7
> > in the sander input-file?
> >
> > It seems to be missing in the AmberManuals
> > http://ambermd.org/doc12/
>
> Same as ntx = 6 but for formatted coordinate files. Probably of not
> much use anymore because ntx = 5 is the more clever variant.
>
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Thank's for the help. :)
Best Regards
Johannes Kalliauer
On 2017-04-11 11:42, Johannes Kalliauer wrote:
> Dear Amber users, Dear Ross Walker,
>
> I am running Amber-Tutorial-B1 (DNA) of Ross Walker.
> I'm am taking his input-files from Section 5:
> http://ambermd.org/tutorials/basic/tutorial1/section5.htm
> and run the commands as written on the website, but the Temperature
> dropped from 300K down to about 200K (See attachment) when
> (immediately after) changing from one Input-File to the next, which
> shouldn't. (tempi = 300.0, temp0 = 300.0,)
>
> I uploaded my files to:
> http://jokalliauer.bplaced.net/live%20access/Internet/UNI/PhD/B1Win/
> (Alternative everything as ZIP):
> http://jokalliauer.bplaced.net/live%20access/Internet/UNI/PhD/B1Win.zip
> I run the problem with AmberTools16.21 on Cygwin and on Ubuntu 16.04,
> both had the same problem, as mentioned above.
>
> I don't know what I did wrong, because I just downloaded the
> inputfiles (polyAT_wat_min1.in
> <http://ambermd.org/tutorials/basic/tutorial1/files/amber_input_files/polyAT_wat_min1.in>,
> polyAT_wat.prmtop
> <http://ambermd.org/tutorials/basic/tutorial1/files/amber_input_files/polyAT_wat.prmtop>,
> polyAT_wat.inpcrd
> <http://ambermd.org/tutorials/basic/tutorial1/files/amber_input_files/polyAT_wat.inpcrd>,
> polyAT_wat_min2.in
> <http://ambermd.org/tutorials/basic/tutorial1/files/amber_input_files/polyAT_wat_min2.in>,
> polyAT_wat_md1.in
> <http://ambermd.org/tutorials/basic/tutorial1/files/amber_input_files/polyAT_wat_md1.in>,
> polyAT_wat_md2.in
> <http://ambermd.org/tutorials/basic/tutorial1/files/amber_input_files/polyAT_wat_md2.in>)
> did not edit anything at all and run the commands as written in the
> tutorial (Sec5.sh
> <http://jokalliauer.bplaced.net/live%20access/Internet/UNI/PhD/B1Win/Sec5.sh>).
> Maybe because I use a newer version of AmberTools (16.21)?
>
> According to Amber16-Manual the restart-file should contain all
> velocities (therefore also the kinetic energy/temperature?), therefore
> I don't understand why it is not working as written in the tutorial.
>
> Best regards from Vienna
> Johannes Kalliauer
> TU Wien (Vienna University of Technology)
>
>
> -------- Weitergeleitete Nachricht --------
> Betreff: Re: Poly(A)-Poly(T) DNA Tutorial Query
> Datum: Thu, 23 Mar 2017 18:32:21 -0400
> Von: Ross Walker <ross.rosswalker.co.uk>
> An: Johannes Kalliauer <johannes.kalliauer.tuwien.ac.at>
>
>
>
> Hi Johannes,
>
> Yes AMBER 16 updated the default restart format to netcdf binary. The
> tutorial needs updating. I'll make that modification now. Thanks for
> pointing that out.
>
> With regards to the prmtop the file format definition is here:
> http://ambermd.org/formats.html
>
> It also has info for the coordinate file etc.
>
> Hope that helps.
>
> All the best
> Ross
>
>> On Mar 23, 2017, at 12:37, Johannes Kalliauer
>> <johannes.kalliauer.tuwien.ac.at
>> <mailto:johannes.kalliauer.tuwien.ac.at>> wrote:
>>
>> Dear Ross Walker,
>>
>> First thank you very much for the Amber-Tutorials. They are really
>> awesome.
>>
>> I have a comment to Section4 of the B1-DNA-Tutorial:
>> http://ambermd.org/tutorials/basic/tutorial1/section4.htm
>> Using the command
>>> $AMBERHOME/bin/sander -O -i polyAT_gb_init_min.in -o
>>> polyAT_gb_init_min.out -c polyAT_vac.inpcrd -p polyAT_vac.prmtop -r
>>> polyAT_gb_init_min.rst
>> leads in my case (Amber16) to a binary restartfile.
>>
>> According to
>> http://archive.ambermd.org/201603/0168.html
>> I had to modify the code for ambpdb from
>>> $AMBERHOME/bin/ambpdb -p polyAT_vac.prmtop *<*
>>> polyAT_gb_init_min.rst > polyAT_gb_init_min.pdb
>> to
>>> $AMBERHOME/bin/ambpdb -p polyAT_vac.prmtop *-c*
>>> polyAT_gb_init_min.rst > polyAT_gb_init_min.pdb
>> so instead of a "<" I used a "-c" and it worked for me.
>>
>> I have a second commend: (Maybe it is a stupid questions, but I think
>> it might be important for my research.)
>> I would like to understand the *.prmtop files better, for example
>> where can I find the definition of the periodic truncated octahedron
>> (size of box, is it periodic/vacuum, which shape,...).
>> Maybe there is a Manual, or an tutorial which explains the
>> prmtop-Strutures.
>>
>> Best Regards
>> Johannes Kalliauer
>> TU Wien (Vienna University of Technology)
>> Austria
>>
>
>
>
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Received on Wed May 03 2017 - 04:00:04 PDT
