Hi,
In addition, consider saving your trajectory in NetCDF format in your
simulations from the start (use input flag ioutfm=1). NetCDF has
higher precision, is less prone to errors, is faster to process, and
VMD can correctly determine whether the trajectory has box info or not
automatically.
-Dan
On Fri, Apr 17, 2015 at 1:32 AM, Karl Kirschner <k.n.kirschner.gmail.com> wrote:
> Hello Pierre,
>
> I believe the problem is how you are reading in the coordinate file into
> VMD. There are two ways to do this - with or without periodic box
> information. When you are in VMD and are within the New Molecule submenu,
> make sure you select the correct file type when loading the trajectory of
> that type (i.e. AMBER Coordinates or AMBER Coordinates with Periodic Box).
> (Know that you need to first load the corresponding topology.) Hopefully,
> this will solve your problem. Alternatively, you can use cpptraj to process
> your trajectory and save it in different formats.
>
> Cheers,
> Karl
>
> On Fri, Apr 17, 2015 at 8:51 AM, Pierre Bertin <bertinp71.gmail.com> wrote:
>
>> Dear users,
>>
>> I am trying to simulate a carbon nanotube in water. There are lot's of
>> papers, so I have the parameters for each field of .frcmod file. I have
>> also generated prmtop and inpcrd file from leap, where I charged ff14SB,
>> gaff and cnt.frcmod (from parmchk2 and then edited to correct some
>> parameters to write papers found and accepted parameters).
>>
>> *The problem* : After the minimisation and heating (300K), when I visualize
>> heat.mdcrd file all carbon atoms are missplaced in the box extremities and
>> waters molecules take the carbon nanotube place... The carbon nanotube is
>> deaaad!
>>
>> This kind of behavior is revelating a wrong force field, right? Do I have
>> to edit a .lib file and charge it with loadOff in leap for the carbon
>> nanotube molecule?
>>
>> Thank you a lot for your time and possible answers o ways to solve this
>> problem!
>>
>>
>> *Pierre BERTIN*
>> Bioinformatics and Biostatistics student (MSc),
>> University Paris-Sud XI, ORSAY.
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> Karl. N. Kirschner, Ph.D.
> Research Associate
> Bonn-Rhein-Sieg University of Applied Sciences
> Grantham-Allee 20, 54757 Sankt Augustin, Germany
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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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
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Received on Fri Apr 17 2015 - 07:30:02 PDT
