[gmx-users] potential energy

[mah maz]

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
>>
>