Hi Prof David,
Thanks for your reply! I have applied update.12(and all other updates in Amber16) and I get this message: ‘update_amber only updates the raw source code! You must recompile if you want any changes to take effect!’ Does it mean I need to recompile my Amber using ‘./configure gnu’ or anything else?
Best regards
Meng Wu
------------------------------
Message: 21
Date: Wed, 9 May 2018 10:20:33 -0400
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Different outputs of external electric field
To: AMBER Mailing List <amber.ambermd.org>
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<20180509142033.ccezeackmctftkus.vpn-client-172-16-8-12.rutgers.edu>
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On Wed, May 09, 2018, Meng Wu wrote:
>
> I am trying to do MD simulations of an channel protein under
> external electric field with Amber16. I have tried both
> 'pmemd.cuda.MPI' and 'pmemd.MPI', and my mdin file is:
Just a quick check: be sure you have applied update.12 to Amber16.
(Don't have any other ideas, since I've never used the external electric
field option myself.)
....dac
------------------------------
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Message: 11
Date: Wed, 9 May 2018 11:05:42 +0000
From: Meng Wu <wumeng.shanghaitech.edu.cn>
Subject: [AMBER] Different outputs of external electric field
To: "amber.ambermd.org" <amber.ambermd.org>
Message-ID: <E2CAE2DF204D5F4E95C4B8C2959FF0C567E84AF4.DAGNODE3>
Content-Type: text/plain; charset="us-ascii"
Dear all,
I am trying to do MD simulations of an channel protein under external electric field with Amber16. I have tried both 'pmemd.cuda.MPI' and 'pmemd.MPI', and my mdin file is:
pro 100ns 303K
&cntrl
imin=0, ntx=5, irest=1,
ntc=2, ntf=2, tol=0.0000001,
nstlim=50000000, dt=0.002,
ntt=3, gamma_ln=1.0, temp0=303.0,
ntpr=5000, ntwr=500000, ntwx=5000, ntwv=-1,
ig=-1,
cut=10.0, ioutfm=1, ntxo=2, iwrap=1,
ntb=1, ntp=0,
efx=0, efy=0, efz=-0.12, efn=0,
watnam='WAT', owtnm='O',
/
/
&ewald
skinnb=3.0,
/
but when I checked the .out file there were some different: in the 'pmemd.cuda.MPI' out file, the 'ELECTRIC_FIELD''s value kept in zero in many steps in the first, then it would gradually grow to the "+Infinity", just like this:
NSTEP = 10255000 TIME(PS) = 27610.000 TEMP(K) = 303.24 PRESS = 0.0
Etot = -68057.3991 EKtot = 27464.4258 EPtot = -95521.8249
BOND = 2641.8273 ANGLE = 10028.1511 DIHED = 7558.8394
1-4 NB = 2469.2339 1-4 EEL = 7062.0337 VDWAALS = 2094.0384
EELEC = -127375.9487 EHBOND = 0.0000 RESTRAINT = 0.0000
ELECTRIC_FIELD = **************
------------------------------------------------------------------------------
wrapping first mol.: -66.43840 0.00000 0.00000
NSTEP = 10260000 TIME(PS) = 27620.000 TEMP(K) = 303.20 PRESS = 0.0
Etot = -68028.8495 EKtot = 27461.3828 EPtot = -95490.2323
BOND = 2584.3159 ANGLE = 10033.4851 DIHED = 7594.3923
1-4 NB = 2494.2889 1-4 EEL = 7091.9296 VDWAALS = 2403.0267
EELEC = -127691.6708 EHBOND = 0.0000 RESTRAINT = 0.0000
ELECTRIC_FIELD = +Infinity
------------------------------------------------------------------------------
Does it mean something wrong with my MD? And in the 'pmemd.MPI' out file, the 'ELECTRIC_FIELD''s value fluctuation within a range, just like this:
NSTEP = 8885000 TIME(PS) = 24870.000 TEMP(K) = 301.42 PRESS = 0.0
Etot = -59638.3315 EKtot = 27299.9628 EPtot = -86938.2944
BOND = 2367.9469 ANGLE = 8325.9974 DIHED = 8114.0441
UB = 2954.2898 IMP = 164.6553 CMAP = -82.2941
1-4 NB = 1623.8485 1-4 EEL = -4644.8509 VDWAALS = -1078.5488
EELEC = -104684.0995 EHBOND = 0.0000 RESTRAINT = 0.0000
ELECTRIC_FIELD = 0.7168
Ewald error estimate: 0.8003E-04
------------------------------------------------------------------------------
NSTEP = 8890000 TIME(PS) = 24880.000 TEMP(K) = 302.11 PRESS = 0.0
Etot = -59500.0051 EKtot = 27362.1009 EPtot = -86862.1061
BOND = 2320.7821 ANGLE = 8416.9251 DIHED = 8118.9015
UB = 2922.7252 IMP = 173.8210 CMAP = -73.7683
1-4 NB = 1612.3679 1-4 EEL = -4692.2531 VDWAALS = -1229.0619
EELEC = -104433.1463 EHBOND = 0.0000 RESTRAINT = 0.0000
ELECTRIC_FIELD = 0.6007
Ewald error estimate: 0.1381E-05
------------------------------------------------------------------------------
In this output the 'ELECTRIC_FIELD''s value kooks more credible, an I right? But I don't know why this different arise just one is in cuda version one is not. Thank you in advance!
All the best,
Meng Wu
------------------------------
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Received on Wed May 09 2018 - 20:30:03 PDT
