Hi,<br>I have performed minimization of ubiquitin in vaccum both in GROMACS and NAMD using CHARMM force field .when i have compared the energy values for first step ,i found that variation in the values<br><br> NAMD (kcal/mol) GROMACS(kcal/mol)<br>
Bond 1929.3647 1928.57<br>pro.dihed <span class="Object" id="OBJ_PREFIX_DWT36">256.1007</span> 345.21<br>imp dihed 10.8044 10.797<br>
potential 1295 1215<br>coloumbic -1483.6554 -1557.72<br>LJ 73.1648 69.445 <br><br>Structure<br>
information NAMD GROMACS<br>atoms 1231 1231<br>bonds 1237 1236<br>dihedrals 3293 3292<br>
Impr dihedrals 204 203<br><br>Though the number of atoms are same ,i did not understand why there is variation in number of bonds,angles and dihedrals leading to difference in energy values. <br>
where i have calculated the coloumbic energy and LJ energy from log file of GROMACS by adding up short range,long range and 14 <a href="http://terms.is">terms.is</a> it the correct way of calculating the total coloumbic and LJ energies to compare them with NAMD coloumbic and LJ values.<br>
<br><br>Any help will be highly appreciated.<br><br><br><br>Rajitha,<br>Ph.D student.<br><br><br><br>