<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class="">
<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 class=""></div>
</div>
</body>
</html>