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 Fri Feb 20 2015 - 13:30:06 PST
