Re: [AMBER] How to deal with monoatomic ion, such as ILs anion

From: Takuya Uto <t.uto.cc.miyazaki-u.ac.jp>
Date: Sat, 23 Apr 2016 18:49:22 +0900

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 - 03:00:03 PDT
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