Hi David,
Thanks for the suggestions.
It looks like ntpr and ntwe (energies) are one time step off from ntwx (coordinates) in AMBER 11. If I do a 100 step trajectory outputting energies and coordinates at each step, the 100th energy output from the trajectory corresponds to the 99th coordinate set. But it looks like pmemd.cuda and sander energies are pretty close, so I will just run pmemd.cuda trajectories through sander to get the gb and pbsa energies.
Thanks!
David
***From mdout
NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 56.72 PRESS = 0.0
Etot = -4390.6911 EKtot = 317.9920 EPtot = -4708.6831
BOND = 143.4297 ANGLE = 423.6953 DIHED = 1361.3736
1-4 NB = 453.5515 1-4 EEL = 5671.5091 VDWAALS = -1224.3309
EELEC = -9510.0005 EGB = -2027.9108 RESTRAINT = 0.0000
------------------------------------------------------------------------------
***From mden
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
L5 EKComTot VIRIAL_x VIRIAL_y VIRIAL_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 dV/dlambda
L0 100 0.2000000000E+00 -.4390691116E+04 0.3179919612E+03
L1 0.5672484192E+02 0.5672484192E+02 -.4708683077E+10 0.1000000000E+01
L2 0.1000000000E+01 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
L3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
L4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
L5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
L6 0.0000000000E+00 -.4708683077E+04 -.1224330887E+04 -.9510000492E+04
L7 0.0000000000E+00 0.1434296502E+03 0.4236953176E+03 0.1361373592E+04
L8 0.4535514633E+03 0.5671509123E+04 0.0000000000E+00 0.0000000000E+00
L9 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
***From re-running sander:
minimizing coord set # 99
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -4.7087E+03 8.3816E+00 4.2625E+01 C 1042
BOND = 143.4293 ANGLE = 423.6951 DIHED = 1361.3739
VDWAALS = -1224.3311 EEL = -9510.0002 EGB = -2027.9102
1-4 VDW = 453.5514 1-4 EEL = 5671.5088 RESTRAINT = 0.0000
minimization completed, ENE= -.47086830E+04 RMS= 0.838156E+01
Begin forwarded message:
> From: "David A. Case" <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Energy and Coordinate Outputs
> Date: March 10, 2012 1:13:00 PM EST
> To: AMBER Mailing List <amber.ambermd.org>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
>
> On Fri, Mar 09, 2012, David Minh wrote:
>>
>> this is why it would
>> be helpful to have the energies output during the run correspond to the
>> coordinates output during the run.
>
> Did you look at the mden file?....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
On Mar 10, 2012, at 1:13 PM, David A. Case wrote:
> On Fri, Mar 09, 2012, David Minh wrote:
>>
>> this is why it would
>> be helpful to have the energies output during the run correspond to the
>> coordinates output during the run.
>
> Did you look at the mden file?....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Mar 12 2012 - 09:00:03 PDT
