[AMBER] asking about mden

From: setyanto md <stwahyudi.md.gmail.com>
Date: Mon, 12 Mar 2012 12:33:57 +0700

Dear amber user and developer

I've seen in mden file from my simulation
L0 Nsteps time(ps) Etot EKinetic
L1 Temp T_solute T_solv Pres_scal_solu
L2 Pres_scal_solv BoxX BoxY BoxZ
L3 volume pres_X pres_Y pres_Z
L4 Pressure EKCoM_x EKCoM_y EKCoM_z
L6 VIRIAL_tot E_pot E_vdw E_el
L7 E_hbon E_bon E_angle E_dih
L8 E_14vdw E_14el E_const E_pol
L9 AV_permMoment AV_indMoment AV_totMoment Density
L0 1000 0.2720000000E+03 -.1208338312E+06 0.3102085216E+05
L1 0.3023337312E+03 0.3023337312E+03 -.1518546833E+12 0.1000000000E+01
L2 0.1000000000E+01 0.8166103625E+02 0.8257414682E+02 0.8364936770E+02
L3 0.5640587728E+06 -.2564075020E+03 -.1010827261E+03 -.5985013636E+02
L4 -.1391134548E+03 0.4437411676E+04 0.4428774486E+04 0.4430832424E+04
L5 0.1329701859E+05 0.5478318045E+04 0.4839127743E+04 0.4673798748E+04
L6 0.1499124454E+05 -.1518546833E+06 0.1712942389E+05 -.1920517007E+06
L7 0.0000000000E+00 0.1199941354E+04 0.3168131530E+04 0.4093965581E+04
L8 0.1399352891E+04 0.1320620212E+05 0.0000000000E+00 0.0000000000E+00
L9 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.9074595185E+00

I want to know about energy electrostatic.
1. What is the different between E_14el and E_el ?
2. How E_el being calculated when simulation ?
3. I'd like to calculate the Energy Electrostatic between 2 residue, can I
use ptraj ? is there any tutorial for this calculation ?

Setyanto Tri Wahyudi
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Received on Sun Mar 11 2012 - 23:00:03 PDT
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