Hi,
On Monday, July 22, 2013, Tanmoy Paul wrote:
> Hi,
> It's Tanmoy here. You are quite right. Now is there any way that I can
> use a box keeping
> 'IGB=1' ?
No. With implicit solvation you don't need periodic boundary conditions
since the solvent is effectively infinite (make sure you use a large enough
cutoff)
-Dan
Please suggest...
>
> Tanmoy
>
>
>
> On Sat, Jul 20, 2013 at 10:37 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com <javascript:;>> wrote:
>
> > It should not jump, but it can move around. That should be fine. Is
> there a
> > problem that you want to avoid by using a box?
> > On Jul 20, 2013 12:05 AM, "Tanmoy Paul" <tanmoy635.gmail.com<javascript:;>>
> wrote:
> >
> > > Hi,
> > > I have been trying to do simulation with implicit solvent. Now the
> > > problem that I have is when I am watching the movie in VMD , the
> > molecules
> > > in the system is jumping from one place to the other. Can we assign any
> > box
> > > dimension to the system with 'igb>0'? Here is the input file that I
> > > have used.
> > > production run for 10ns
> > > &cntrl
> > > imin=0,
> > > irest=1,
> > > ntx=5,
> > > ntb=0,
> > > igb=1,
> > > ntc=2,ntf=2,
> > > ntt=3,gamma_ln=1.0,
> > > temp0=298.0,
> > > nstlim=5000000,dt=0.002,
> > > ntpr=100,ntwx=100,ntwr=50000,
> > > cut=15
> > > /
> > > I am eagerly waiting for useful suggestions.
> > >
> > > Thanks
> > >
> > > Tanmoy
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Jul 23 2013 - 06:30:02 PDT
