Hi Bill,
Yes, you are right. Short time may cause problems. In another test, I used 50000 steps. It also has the same problem. I found that no matter what temperature annealing I used, it always stayed at 300 K. Below is an example:
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 - 09:30:02 PST
