# Re: [AMBER] Question about QM/MM simulation in vacuum connecting Amber and Gaussian 09 package

From: Roitberg,Adrian E <roitberg.ufl.edu>
Date: Tue, 9 Apr 2019 00:41:56 +0000

your thermostat has a gamma of zero, which means it is not doing anything. set it to at least 1, maybe 5

Sent from my iPad

> On Apr 8, 2019, at 20:37, 王婷婷 <ttwang.mail.dlut.edu.cn> wrote:
>
> Recently, I performed QM/MD simulation of two molecules in vacuum with igb=6. I set the system temperature at 300K, however, the average temperature of the simulation, which I found at the end of the simulation output file, is quiet abnormal.
>
> I performed two simulations in vacuum. The first is in pure vacuum, and the average temperature of system is about 470K. The second is also in vacuum and extra electric field was added (dielc=78.5), a more dramatic change in temperature was observed and the average temperature of this system is about 2000K !
>
> I’m quiet confused about this unusual phenomenon. I send this e-mail for your help, I want to know why the system temperature varied so huge. Is it normal and can be used for further analysis?
>
> And If there is something wrong, how can I put the temperature stable.
>
>
>
> Here is the input：
> 【vacuum/e=78.5】
>
> 300K constant temp QMMMMD
> &cntrl
> imin = 0, irest=0,ntx=1,
> ntb = 0,
> igb= 6 ,
> dielc= 78.5 ,
> cut = 9.0,ntx=1,
> tempi = 298.0, temp0 = 298.0,
> ntt = 3, gamma_ln = 0,
> nstlim = 20000, dt = 0.001,
> ntpr = 20, ntwx = 20 , ntwr = 20
> ntc=2, ntf=2,nmropt=1, ifqnt=1,
> /
> &wt type='DUMPFREQ', istep1=100 /
> &wt type='END' /
> DISANG=N-C-5.0.RST
> DUMPAVE=N-C-15.0-rstN.out
> /
> &qmmm
> qmmask=':1-2'
> qmcharge=0,
> qm_theory='EXTERN',
> qmshake=0,
> qmcut=12.0,
> qm_ewald=0
> /
>
> &gau
> method = 'B3LYP'
> basis = '6-31+G**'
> num_threads=16
> charge = 0
> scf_conv=6
> &end
>
>
> 【pure vacuum】
>
> 300K constant temp QMMMMD
> &cntrl
> imin = 0, irest=0,ntx=1,
> ntb = 0,
> igb=6,
> cut = 9.0,ntx=1,
> tempi = 298.0, temp0 = 298.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 10000, dt = 0.001,
> ntpr = 20, ntwx = 20 , ntwr = 20
> ntc=2, ntf=2,nmropt=1, ifqnt=1,
> /
> &wt type='DUMPFREQ', istep1=100 /
> &wt type='END' /
> DISANG=N-C-5.0.RST
> DUMPAVE=N-C-15.0-rstN.out
> /
> &qmmm
> qmmask=':1-2'
> qmcharge=0,
> qm_theory='EXTERN',
> qmshake=0,
> qmcut=12.0,
> qm_ewald=0
> /
>
> &gau
> method = 'B3LYP'
> basis = '6-31+G**'
> num_threads=16
> charge = 0
> scf_conv=6
> &end
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------------
> 王婷婷
> 大连理工大学工业生态与环境工程教育部重点实验室
> 地址：辽宁省大连市甘井子区凌工路2号 环境楼
> 邮编：116024
> 电话：183-4223-5107
> Tingting Wang
> Key Laboratory of Industrial Ecology and Environmental Engineering (MOE) , CHINA
> School of Environmental Science and Technology, Dalian University of Technology Dalian, CHINA
>
> 116024,P. R.
> Phone Number: +86 183-4223-5107
>
> E-mail: ttwang.mail.dlut.edu.cn
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=9af5c5_dapVXsXlecwF3QFwfFJYZZnsWJgMM7hRtD9s&s=mjHYzg8nuGgkLXWkHxYKaHRHsOenwTqgo3BTZgSZJm0&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 08 2019 - 18:00:04 PDT
Custom Search