[gmx-users] potential energy

[mah maz]

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
>