AMBER Archive (2005)

Subject: Re: AMBER: periodicity problem

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Mar 16 2005 - 15:25:39 CST

Hi Julie,

I am not sure if you can use ntb=1 (Constant volume) if you are in vacuo.
if there is not any solvent present, why to have a boundary? If you
solvate the system with TIP3P Water box, then it is reasonable to have a
constant volume or pressure condition (ntb=1 or 2). I would suggest u to
solvate it with the right box size: (I am always using 'solvateoct
<molecule name> TIP3PBOX 12.0' so that I have use the cut=8 condition in
the MD simulation)

By the way, I am assuming that you want to do a 150 ps simulation, but
this is just 2 ps.

Good luck,

On Wed, 16 Mar 2005, Stern, Julie wrote:

> Hello Amber-onians,
>
> I'm working on an alkane chain problem in vacuo. I set the box for
> periodicity
> with setBox vdw in leap and have tried various versions of periodicity
> during
> the equilibration but it doesn't work. What I'm seeing (vmd) are the atoms
> fixed to
> a certain part of the screen and then bonds becoming really long as the
> alkane
> chain apparantly shows up on the other side (it's aesthetic but not
> scientific),
> and only with ntb = 0 do I get a normal looking chain.
> During equilibration, I've tried ntb = 1, ntb = 2 along with ntp =
> 1,
> ntb = 2 along with ntp =2 and still the same affect. I've tried it with and
> without
> shake on so that would be ntf = 1, ntc = 1 or with ntf = 2, ntc =2, but that
> didn't
> change anything. During minimization I was able to use ntb = 1 and turn of
> PME, but that didn't work for equilibration either.
> The equilibration input file is:
>
> Equilibration: 150 ps MD
> &cntrl
> imin = 0, irest = 0,
> ntx = 1, ntb = 1,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 2000, dt = 0.001,
> ntpr = 100, ntwx = 100, ntwr = 1000,
> cut = 8, ntr=0,
> ntf = 1, ntc = 1,
> ibelly = 1,
> bellymask = '!@SA',
> &end
>
>
> Is there anything I can do? What suggestions do you have?
>
> Thanks.
>
> --Julie
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, # B10        -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  - http://www.pas.rochester.edu/~yildirim/                     -
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