Re: [AMBER] Different potential energies between recomputed and original simulations from PMEMD?

From: 杨明俊 <mjyang.dicp.ac.cn>
Date: Fri, 24 May 2019 20:02:28 +0800 (GMT+08:00)

Hi All,

   Sorry that I made a stupid mistake about the BOX setting in the extracted coordinate file from the trajectory. By using correct BOX size, now everything is correct.

Best,

Mingjun


> -----Original Messages-----
> From: "杨明俊" <mjyang.dicp.ac.cn>
> Sent Time: 2019-05-24 18:14:32 (Friday)
> To: amber.ambermd.org
> Cc:
> Subject: [AMBER] Different potential energies between recomputed and original simulations from PMEMD?
>
> Hi All,
>
>
> I am trying to recompute the energies using PMEMD for individual frames from a trajectory generated from a previous PMEMD simulation (under NVT ensemble). However, I get very different VDWAALS and EELEC energies between the recomputed ones and the ones printed in original simulation. Does anyone know how this big difference comes from? It seems different pairlist shouldn't produce such a large different values.
>
>
> In order to show this problem, I made a simple test using the following scripts (see below). From the comparison, the bonded terms are very close to each other. However, the nonbonded terms (VDWAALS and EELEC) are very different from the original simulation and recomputed simulation.
>
>
> Is there a way that I can get the same recomputed energies as the ones printed from the original simulation with PMEMD? Any suggestion or explanation is greatly appreciated.
>
>
> Big thanks!
>
>
> Mingjun
>
>
>
>
>
>
> ------------------trajectory generation: 4 frames were recorded from this simulation
> test md simulations
> &cntrl
>
>
> ! parameters for general MD
> imin = 0, nstlim = 200, irest = 0, dt = 0.002,
> ntt = 3, temp0 = 298.0, gamma_ln = 2.0, ig = -1,
> ntb = 1, mcbarint = 1,
> ntp = 0, barostat = 2, pres0 = 1.01325, taup = 2.0,
> ntwe = 10, ntwx = 50, ntpr = 1, ntwr = 10, ntave = 10,
> ioutfm = 1, iwrap = 1, ntxo = 2,
>
> ntc = 2, ntf = 1,
>
> /
> &ewald
> /
> ----------------------The energy components for the 3rd recorded frame:
> NSTEP = 151 TIME(PS) = 0.302 TEMP(K) = 230.95 PRESS = 0.0
> Etot = -144574.8836 EKtot = 24867.1203 EPtot = -169442.0039
> BOND = 907.5497 ANGLE = 2519.4685 DIHED = 4651.2401
> 1-4 NB = 1345.9908 1-4 EEL = 16351.0887 VDWAALS = 21141.9669
> EELEC = -216359.3087 EHBOND = 0.0000 RESTRAINT = 0.0000
> Ewald error estimate: 0.3404E-04
>
>
>
> =====================PMEMD rerun with the 3rd frame generated from above simulation
> rerun md simulations
> &cntrl
>
>
> ! parameters for general MD
> imin = 0, nstlim = 2, irest = 0, dt = 0.002,
> ntt = 3, temp0 = 298.0, gamma_ln = 2.0, ig = -1,
> ntb = 1, mcbarint = 1,
> ntp = 0, barostat = 2, pres0 = 1.01325, taup = 2.0,
> ntwe = 10, ntwx = 50, ntpr = 1, ntwr = 10, ntave = 10,
> ioutfm = 1, iwrap = 1, ntxo = 2,
>
> ntc = 2, ntf = 1,
>
> /
> &ewald
> /
> ----------------------The energy components for step 0 with the 3rd recorded frame:
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
> Etot = -158202.8866 EKtot = 0.0000 EPtot = -158202.8866
> BOND = 907.5465 ANGLE = 2519.4674 DIHED = 4651.2408
> 1-4 NB = 1345.9908 1-4 EEL = 16351.0884 VDWAALS = 20307.6375
> EELEC = -204285.8579 EHBOND = 0.0000 RESTRAINT = 0.0000
> Ewald error estimate: 0.4939E-04
> ----------------------
>
>
>
>
>
>
>
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Received on Fri May 24 2019 - 05:30:03 PDT
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