Thank you!
I ran a 1 step molecular dynamics simulation and i did get a mden file. But
I guess the energies in it are not what I wanted.
I want to get the energy and actual bond length of each bond in the system.
Is there a way to receive such data using Amber? (I have a mismatch in the
bond energy while calculating it in Amber and in another program and I
wanted to see if I can identify the bond which causes it).
Yocheved
On Tue, Nov 27, 2012 at 3:27 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> On Tue, Nov 27, 2012 at 4:23 AM, יוכבד <ybaime.gmail.com> wrote:
>
>> Hi
>>
>> Is there a way to receive the energies and actual bond lengths of all
>> bonds
>> in a structure while running a single point energy calculation?
>> I tried using ntwe=1 and -e mden but I receive an empty file.
>>
>
> Try running molecular dynamics with 1 step. ntwe only prints out energies
> for dynamics calculations, not minimizations. If all you want is a
> single-point energy (and not a minimized structure), then a single-step MD
> simulation with ntwe=1 should do the trick.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
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Received on Wed Nov 28 2012 - 01:00:02 PST
