[gmx-users] potential energy

[mah maz]

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 <mahmaz71 at 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 <mahmaz71 at 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 <mahmaz71 at 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
> >>
> >
>