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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Received on Sat Apr 23 2016 - 12:00:06 PDT
