Dear Sir
Thank you very much for your reply.
I sincerely thank you . I have finally been overcome the error.
I was equilibrated at low temperatures without the periodic boundary
conditions .
It is a small system of about 2,000 atoms and net charge = 0.
As of advice , it was calculated in the sander.
Really pleased under .. kindly support .Thank you !
Best regards
Takuya Uto
> Date: Sat, 23 Apr 2016 11:50:33 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] How to deal with monoatomic ion, such as ILs
> anion
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <571BC3F9.2060007.cgl.ucsf.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> By the way, what's the net charge on your system? How many total atoms?
> It might be interesting to try it without periodic boundaries.
> Odd that vdw and bond would blow up, but not electrostatics.
>
> Bill
>
> On 4/23/16 11:41 AM, Andrew Schaub wrote:
> > I've been running equilibrations using sander (MPI), then I switch to
pmemd
> > for production runs. Maybe run md1 (which is a 3 ns equilibration) using
> > sander (MPI)?
> >
> > Best Regards,
> >
> > Andrew
> >
> > On Sat, Apr 23, 2016 at 11:30 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> You could try dropping you starting temperature further, even to 1. I
> >> would also save every frame, and watch the animation for clues.
> >>
> >> Bill
> >>
> >> On 4/23/16 2:49 AM, Takuya Uto wrote:
> >>> Thank you for your suggestion.
> >>>
> >>> Although I have tried to do the calculations in NTV it does not work.
> >>>
> >>> The input file and out file is shown below .
> >>>
> >>> I use GPU Version of PMEMD.cuda module.
> >>>
> >>> I understand that the equilibration process is bad as you pointed out.
> >>>
> >>> However , I do not know whether any protocol is good . Please help me.
> >>>
> >>>
> >>>
> >>> Best regards.
> >>>
> >>> Takuya Uto
> >>>
> >>>
> >>>
> >>> #### md input ######################
> >>>
> >>> molecular dynamics
> >>>
> >>> &cntrl
> >>>
> >>> imin = 0, irest = 0, ntx = 1,
> >>>
> >>> ntb = 1, cut = 14.0 , iwrap = 0,
> >>>
> >>> ntt = 3, gamma_ln = 5.0 ,
> >>>
> >>> tempi = 20.0, temp0 = 20.0,
> >>>
> >>> nstlim = 1000000, dt = 0.0001,
> >>>
> >>> ntpr = 100, ntwx = 100, ntwr = 100,
> >>>
> >>> &end
> >>>
> >>> ##################################
> >>>
> >>>
> >>>
> >>> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 20.00
> PRESS =
> >>> 0.0
> >>>
> >>> Etot = -2459.3191 EKtot = 125.2190 EPtot =
> >>> -2584.5381
> >>>
> >>> BOND = 25.7564 ANGLE = 729.3448 DIHED
> =
> >>> 74.6309
> >>>
> >>> 1-4 NB = 71.3685 1-4 EEL = -517.5268 VDWAALS =
> >>> -424.0162
> >>>
> >>> EELEC = -2544.0957 EHBOND = 0.0000 RESTRAINT
> =
> >>> 0.0000
> >>>
> >>>
> >>
>
---------------------------------------------------------------------------
> -
> >>> --
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> NSTEP = 100 TIME(PS) = 0.010 TEMP(K) =*********
> PRESS =
> >>> 0.0
> >>>
> >>> Etot = ************** EKtot = ************** EPtot =
> >>> **************
> >>>
> >>> BOND = ************** ANGLE = 208168.0251 DIHED
> =
> >>> 7293.6233
> >>>
> >>> 1-4 NB = -0.0000 1-4 EEL = -0.0876 VDWAALS =
> >>> **************
> >>>
> >>> EELEC = -2395.0676 EHBOND = 0.0000 RESTRAINT
> =
> >>> 0.0000
> >>>
> >>>
> >>
>
---------------------------------------------------------------------------
> -
> >>> --
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> NSTEP = 200 TIME(PS) = 0.020 TEMP(K) =*********
> PRESS =
> >>> 0.0
> >>>
> >>> Etot = ************** EKtot = ************** EPtot =
> >>> **************
> >>>
> >>> BOND = ************** ANGLE = 144728.1573 DIHED
> =
> >>> 7627.9577
> >>>
> >>> 1-4 NB = 0.0000 1-4 EEL = -0.1720 VDWAALS =
> >>> **************
> >>>
> >>> EELEC = -1513.7364 EHBOND = 0.0000 RESTRAINT
> =
> >>> 0.0000
> >>>
> >>>
> >>
>
---------------------------------------------------------------------------
> -
> >>> --
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> From: Takuya Uto [mailto:t.uto.cc.miyazaki-u.ac.jp]
> >>> Sent: Saturday, April 23, 2016 6:29 PM
> >>> To: 'Takuya Uto' <t.uto.cc.miyazaki-u.ac.jp
> >>> <mailto:t.uto.cc.miyazaki-u.ac.jp> >
> >>> Subject:
> >>>
> >>>
> >>>
> >>> From: kurisaki <kurisaki.ncube.human.nagoya-u.ac.jp
> >>> <mailto:kurisaki.ncube.human.nagoya-u.ac.jp
> >> ?Subject=Re%3A%20%5BAMBER%5D%20Ho
> >>>
> w%20to%20deal%20with%20monoatomic%20ion%2C%20such%20as%20ILs%
> 20anion> >
> >>> Date: Fri, 22 Apr 2016 10:57:39 +0900
> >>>
> >>>
> >>> Before you execute production runs,
> >>> How about relaxing the system more carefully?
> >>> For example, use a smaller integration steps (0.01 ps)
> >>> and NVT simulation:
> >>> NPT simulation might make steric crash
> >>> and cause anomalous energy raise,
> >>> If the system is not sufficiently 'relaxed'.
> >>>
> >>> My best,
> >>>
> >>> IK
> >>>
> >>>
> >>>
> >>> From: Bill Ross <
> >>> <mailto:ross.cgl.ucsf.edu
> >> ?Subject=Re%3A%20%5BAMBER%5D%20How%20to%20deal%20wi
> >>> th%20monoatomic%20ion%2C%20such%20as%20ILs%20cation>
> ross.cgl.ucsf.edu>
> >>> Date: Thu, 21 Apr 2016 18:39:21 -0700
> >>>
> >>>
> >>> What is the error you encountered? I suggest posting the text and your
> >>> md input.
> >>>
> >>> Usually such complaints are due to bad equilibration protocols.
> >>>
> >>> Bill
> >>>
> >>> On 4/21/16 6:29 PM, Takuya Uto wrote:
> >>>> Dear Sir
> >>>>
> >>>>
> >>>>
> >>>> Currently , I try the simulation using the typical ionic liquid, such
as
> >>>> [BMIM][Cl] etc...
> >>>>
> >>>> It has followed the TUTORIAL A15. LEaP and minimization works are
> going
> >>>> well.
> >>>>
> >>>> But, I have encountered an error in the MD calculation.
> >>>>
> >>>> I have it two points that you want to ask .
> >>>>
> >>>> 1. Is it difficult for AMBER software to calculate a large number of
> >>>> monoatomic ion.
> >>>>
> >>>> 2. Cl- parameters were applied parameters of Li et al . Is this wrong
?
> >>>>
> >>>>
> >>>>
> >>>> Regards.
> >>>>
> >>>> Takuya Uto
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 24.24 PRESS =
> >>>> 0.0
> >>>>
> >>>> Etot = -2461.6391 EKtot = 125.2190 EPtot =
> >>>> -2586.8582
> >>>>
> >>>> BOND = 22.7264 ANGLE = 729.3448 DIHED =
> >>>> 74.6309
> >>>>
> >>>> 1-4 NB = 71.3685 1-4 EEL = -517.5268 VDWAALS =
> >>>> -423.1190
> >>>>
> >>>> EELEC = -2544.2829 EHBOND = 0.0000 RESTRAINT =
> >>>> 0.0000
> >>>>
> >>>>
> >>
>
---------------------------------------------------------------------------
> -
> >>>> --
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> NSTEP = 500 TIME(PS) = 1.000 TEMP(K) =********* PRESS =
> >>>> 0.0
> >>>>
> >>>> Etot = ************** EKtot = ************** EPtot =
> >>>> **************
> >>>>
> >>>> BOND = -0.0000 ANGLE = 184688.7258 DIHED =
> >>>> 7322.8481
> >>>>
> >>>> 1-4 NB = 0.0000 1-4 EEL = 0.0003 VDWAALS =
> >>>> **************
> >>>>
> >>>> EELEC = -2577.3284 EHBOND = 0.0000 RESTRAINT =
> >>>> 0.0000
> >>>>
> >>>>
> >>
>
---------------------------------------------------------------------------
> -
> >>>> --
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) =********* PRESS =
> >>>> 0.0
> >>>>
> >>>> Etot = ************** EKtot = ************** EPtot =
> >>>> **************
> >>>>
> >>>> BOND = -0.0000 ANGLE = 188853.5435 DIHED =
> >>>> 7524.3485
> >>>>
> >>>> 1-4 NB = 0.0000 1-4 EEL = 0.0001 VDWAALS =
> >>>> **************
> >>>>
> >>>> EELEC = -1385.1898 EHBOND = 0.0000 RESTRAINT =
> >>>> 0.0000
> >>>>
> >>>>
> >>
>
---------------------------------------------------------------------------
> -
> >>>> --
> >>>>
> >>>> _______________________________________________
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> >>>> AMBER.ambermd.org
> >>>> <http://lists.ambermd.org/mailman/listinfo/amber>
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>>
> >>> _______________________________________________
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> >>
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Received on Mon Apr 25 2016 - 04:00:05 PDT
