Dear Bogdan, Actually I have generated CNT from a garphene sheet myself. The last question reflects that! Thanks alot for answering all the questions and useful points you mentioned.
Regards, Mah On Tue, Jan 20, 2015 at 10:43 PM, mah maz <mahma...@gmail.com> wrote: > Dear Justin, > > Thank you very much for your beneficial analysis. The problem is not > solved completely but the situation is improved for sure. Your help is > always precious. > > Best Regards, > Mah > > On 1/16/15, mah maz <mahma...@gmail.com> wrote: > > Hi Justin, > > I haven't come to a conclusion yet and need your help! I attached a copy > of > > a typical g_energy -f ener.edr -o copied from terminal and an .mdp file. > > > > Bond 18506.5 50 1625.68 -301.714 > > (kJ/mol) > > Angle 9839.32 13 580.506 -30.2625 > > (kJ/mol) > > Proper Dih. 60199.3 23 845.936 106.894 > > (kJ/mol) > > LJ-14 40461.9 41 1748.27 -227.144 > > (kJ/mol) > > Coulomb-14 0 0 0 0 > > (kJ/mol) > > LJ (SR) -10117.7 2.6 118.855 -3.85515 > > (kJ/mol) > > Coulomb (SR) -156.169 9 40.823 35.6671 > > (kJ/mol) > > Potential 118733 74 1142.65 -420.414 > > (kJ/mol) > > Kinetic En. 14932.1 7.3 423.825 -50.1192 > > (kJ/mol) > > Total Energy 133665 81 1221.66 -470.533 > > (kJ/mol) > > Conserved En. 180812 57 121.277 397.186 > > (kJ/mol) > > Temperature 295.064 0.14 8.37495 -0.990376 (K) > > Pressure -0.072961 0.17 17.163 -0.120159 > (bar) > > Vir-XX 4860.45 210 21707.3 26.9299 > > (kJ/mol) > > Vir-XY 4.73233 3.3 1176.9 -2.74323 > > (kJ/mol) > > Vir-XZ 3.18097 7.5 1907.36 4.2031 > > (kJ/mol) > > Vir-YX 4.73147 3.3 1176.89 -2.74818 > > (kJ/mol) > > Vir-YY 5388.86 39 5500.8 202.824 > > (kJ/mol) > > Vir-YZ 0.0509392 3.2 1101.97 3.89409 > > (kJ/mol) > > Vir-ZX 3.18089 7.5 1907.36 4.19967 > > (kJ/mol) > > Vir-ZY 0.0514236 3.2 1101.97 3.89442 > > (kJ/mol) > > Vir-ZZ 4871.76 200 21686.4 31.3387 > > (kJ/mol) > > Pres-XX 0.156061 0.25 25.1574 -0.125195 > (bar) > > Pres-XY -0.00268517 0.0033 1.36879 0.00150158 > > (bar) > > Pres-XZ -0.00196111 0.0098 2.21263 -0.0154319 > > (bar) > > Pres-YX -0.00268417 0.0033 1.36879 0.00150732 > > (bar) > > Pres-YY -0.511872 0.019 6.38934 -0.0849178 > (bar) > > Pres-YZ 0.000542369 0.0017 1.27895 0.00355122 > > (bar) > > Pres-ZX -0.00196102 0.0098 2.21263 -0.0154279 > > (bar) > > Pres-ZY 0.000541808 0.0017 1.27895 0.00355084 > > (bar) > > Pres-ZZ 0.136928 0.24 25.1334 -0.150365 > (bar) > > #Surf*SurfTen 8.81535 3.2 359.945 -1.26863 > (bar > > nm) > > T-CNT 295.063 0.14 8.44198 -0.997647 (K) > > T-grp1 295.202 0.21 38.5349 0.485478 (K) > > T-grp2 294.688 0.32 53.7236 -2.39488 (K) > > > > > > > > dt = 0.0001 > > tinit = 0 > > nsteps = 2000000 > > nstxout = 1000 > > nstvout = 1000 > > nstfout = 0 > > nstlog = 1000 > > nstenergy = 1000 > > nstlist = 5 > > ns_type = grid > > rlist = 0.9 > > coulombtype = cutoff > > rcoulomb = 0.9 > > rvdw = 0.9 > > pbc = xyz > > integrator = md-vv > > Tcoupl = nose-hoover > > tau_t = 0.1 0.1 0.1 > > ref_t = 295 295 295 > > tc_grps = CNT grp1 grp2 > > gen_temp = 295 > > > > Your answer to any of these questions would be a ton of help! > > These potential energies are the average ones, how can I get the final > > potential of the system? Are average potentials good terms to decide if > the > > simulation was wrong? > > Can the positive potentials be the effect of forcefield inappropriate > > files? > > The system is a CNT containing some solvent. Can positive potentials be > the > > reflection of the system's angle pressure not willing to reform from > plane > > graphene system? > > > > I would appreciate your help. Many thanks in advance! > > Regards, > > Mah > > > > > > > > > > > > On Sun, Jan 11, 2015 at 5:31 PM, mah maz <mahma...@gmail.com> wrote: > > > >> Hi Justin, > >> That's right in the .edr I have more than these 4 terms, I just > mentioned > >> the terms related to energy of the system.The output file is a large one > >> not in a proper format to be sent, but can be attached if possible. > >> That was a great deal of help up to this point. > >> Thank you very much! > >> Regards, > >> Mah > >> > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.