Hi Albert,
I think the 'diffusing' of the water molecules is a different issue, and
not really an issue at all; AMBER programs (sander,pmemd etc.) by default
'follow' the water molecules as they traverse periodic boundaries, i.e. no
re-imaging is done on the fly. If you do want this to happen, use iwrap=1
in your input.
(which may be good if you want to run really long simulations anyway, where
coordinates of water molecules may become too large for restart files.)
You can use the 'image' commands in ptraj to do 'wrap' the water molecules
into a box around your solute for trajectories obtained with the default
iwrap=0.
See related issues on the mailing list and section 2.5.3 in the AMBER 12
manual (iwrap) as well as the ptraj documentation (for imaging) for further
explanations.
--Marc
On 10 May 2012 08:33, Albert <mailmd2011.gmail.com> wrote:
> Hi Marc:
>
> I am not sure about this, because each time after NVT, I found that
> my water molecules doesn't stay in the same box, it diffused...... here
> is my NVT input file:
>
>
> heating gradually over 300ps
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=300000,dt=0.001,
> ntc=2,ntf=2,
> cut=10.0, ntb=1,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0,
> tempi=0.0, temp0=310.0,
> restraintmask=':1-677 & !.H=',
> restraint_wt=10.0,
> nmropt=1
> /
> &wt TYPE='TEMP0', istep1=0, istep2=300000,
> value1=0.1, value2=310.0, /
> &wt TYPE='END' /
>
>
>
> On 05/10/2012 09:30 AM, Marc van der Kamp wrote:
> > Sounds like something for the VMD mailing list...
> > Marc
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 10 2012 - 01:30:04 PDT
