Hi,
I think in this case it may help to see your system. Can you send me
off-list your topology and restart files? Thanks.
-Dan
On Fri, Feb 20, 2015 at 2:04 PM, Zhang, Sixue <szhang74.illinois.edu> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Feb 20 2015 - 13:30:06 PST
