On 1/16/15 8:56 AM, mah maz 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?
The .edr file contains energies at every nstenergy steps. An instantaneous value is not terribly useful, though.
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?
The outcome indicates that the potential energy is dominated by bonded (i.e. intramolecular) interactions, while there are few/weak nonbonded interactions among the atoms in the system. If I'm interpreting what you're saying, there is some solvent inside the CNT, and nothing outside? Generally, most condensed phase systems (at least those in water) are dominated by electrostatic interactions, whereas your system has a negligible amount of electrostatics. The overall effect is a function of what your species are. But for that, you're going to have to tell us what "grp1" and "grp2" are, what their topologies are, etc.
But in reality, there seems to be nothing "wrong" with the simulation; it's just atypical, and you can't really compare it to a "normal" simulation with a lot of water.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
