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>