On Sat, Feb 21, 2015 at 11:21 AM, Zhang, Sixue <szhang74.illinois.edu> wrote:
> I found that no matter what temperature annealing I used, it always
> stayed at 300 K. Below is an example:
You are attempting to vary TEMP0, but you did not set temp0 initially.
If I remember correctly, adding temp0=500, to your &ctrl namelist will
fix this problem.
> solvent NVT equilibritaion
> &cntrl
> nstlim=640000, dt=0.001, ntpr=1000, ntwr=1000, ntwx=1000, iwrap=1,
> tempi=0, ntt=3, imin=0,
> ntb=1, cut=12.0, ig=-1, ntc=2, ntf=2, gamma_ln=2.0,
> ioutfm=1, ntwv=-1, ntr=1, restraintmask=':1-155', restraint_wt=100.0
> /
> &wt TYPE='TEMP0', restraint_wt=100.0, istep1=0, istep2=10000,
> value1=0, value2=300.0, /
> &wt TYPE='TEMP0', restraint_wt=100.0, istep1=10001, istep2=60000,
> value1=300.0, value2=300.0, /
> &wt TYPE='TEMP0', restraint_wt=100.0, istep1=60001, istep2=70000,
> value1=300.0, value2=500.0, /
> &wt TYPE='TEMP0', restraint_wt=100.0, istep1=70001, istep2=120000,
> value1=500.0, value2=500.0, /
>
> Thanks
>
> Sixue
>
> -----Original Message-----
> From: Bill Ross [mailto:ross.cgl.ucsf.edu]
> Sent: Friday, February 20, 2015 4:02 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Solvent Box Wrapping Issue
>
> 5000 steps seems like a short time to go 0-300K. I'd try increasing that by a factor of 10. Fast warming can lead to problems.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: "Zhang, Sixue" <szhang74.illinois.edu> </div><div>Date:02/20/2015 1:04 PM (GMT-08:00) </div><div>To: amber.ambermd.org </div><div>Subject: [AMBER] Solvent Box Wrapping Issue </div><div> </div>Hello,
>
> I found my solvent box became into a very weird shape after dynamics. I used a rectangular TIP3P box and ran an either NVT or NPT equilibration with restraints on my solute. After equilibration, there is no waters at the eight corners of the solvent box. The transition is very shape, which makes me believe it is a wrapping issue. I tested a pure water box. It has the same issue when I use Sander.MPI or pmemd.MPI to run the dynamics. I tried iwrap=1 in the input file and post-wrapping by cpptraj. None of them helps. Below is an example of my input file. Does anyone have an idea about this problem?
>
> equilibritaion
> &cntrl
> nstlim=10000, dt=0.002, ntpr=500, ntwr=5000, ntwx= 5000, tempi=0, temp0=300.0, ntt=3, imin=0, iwrap=1, ntb=1, cut=8, ig=-1, ntc=2, ntf=2, gamma_ln=2.0, ioutfm=1, ntwv=-1, ntr=1, restraintmask=':1-155', restraint_wt=10.0 / &wt TYPE='TEMP0', restraint_wt=10.0, istep1=0, istep2=5000, value1=0, value2=300.0, / &wt TYPE='TEMP0', restraint_wt=1.0, istep1=5001, istep2=10000, value1=300.0, value2=300.0, / &wt TYPE='END' / Thanks a lot!
> Sixue Zhang
> University of Illinois at Urbana-Champaign
> A414 Chemical & Life Sciences Laboratory
> 600 S Mathews Avenue, Urbana, IL, 61801
> Office phone:217-300-1480
> Email: szhang74.illinois.edu<mailto:szhang74.illinois.edu>
> zhangsixue1816.outlook.com<mailto:zhangsixue1816.outlook.com>
> 760265580.qq.com<mailto:760265580.qq.com>
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Received on Sat Feb 21 2015 - 14:30:05 PST
