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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Received on Sat Apr 23 2016 - 12:00:04 PDT
