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<div class="moz-cite-prefix">Hi,<br>
<br>
The total energy will never be conserved perfectly. How good it is
conserved depends on the time step.<br>
But it seems, although it's not clear from your mail, that you are
talking about your own program. This is a mailing list for
problems with Gromacs relatead problems, not for help with your
own code. All I can add is that most bugs in an MD code will cause
to total energy to increase.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 05/10/2016 05:57 AM, #CHEN WENJIE# wrote:<br>
</div>
<blockquote
cite="mid:53E6E160-4260-4ED0-923F-4D74BDFB7696@e.ntu.edu.sg"
type="cite">
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<div class="" style="margin: 0px; line-height: normal; color:
rgb(69, 69, 69);">Hi GROMACS team,</div>
<div class="" style="margin: 0px; line-height: normal; color:
rgb(69, 69, 69);"><br class="">
</div>
<div class="" style="margin: 0px; line-height: normal; color:
rgb(69, 69, 69);">I am an undergraduate student from Nanyang
Technological University. I am working on my MD physics engine
project that replicates some of the GROMACS features. The
programming language is Java. The project is to simulate some
small molecules in atomic level. The topology file is
generated by GROMACS with pdb2gmx program. The force field I
choose is AMBER03, and force field parameters are also from
GROMACS. I use Velocity Verlet integrator. </div>
<div class="" style="margin: 0px; line-height: normal; color:
rgb(69, 69, 69);">The problem I encounter is that when I run
the simulation, the total energy doesn't conserve. It
increases a little bit every frame and eventually becomes huge
and the molecule deforms.</div>
<div class="" style="margin: 0px; line-height: normal; color:
rgb(69, 69, 69); min-height: 14px;">
<br class="">
</div>
<div class="" style="margin: 0px; line-height: normal; color:
rgb(69, 69, 69);">Attached is my GRO file and TOP file, and
some log output files for the simulation of water molecule.
One only involves bond stretching energy. One only involves
angle rotation energy. One involves both bond and angle
energy. For each frame, I log the kinetic energy, potential
energy, total energy and position of each atom. Although when
Ep increases, Ek will decrease, and vice versa, the total
energy increases a little bit each frame. </div>
<div class="" style="margin: 0px; line-height: normal; color:
rgb(69, 69, 69); min-height: 14px;">
<br class="">
</div>
<div class="" style="margin: 0px; line-height: normal; color:
rgb(69, 69, 69);">I really want to know if there is any part I
miss out or didn't do it correctly. I really appreciate it if
you can give me some advice. Thank you in advice.</div>
</div>
<br class="">
<div class="">
<div class="">Best regards,</div>
<div class="">Wenjie</div>
<div class=""><br class="">
</div>
</div>
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