if you don't wrap coordinates during MD then the waters will diffuse away.
this is not a problem as it is handled through the periodicity.
use ptraj to image the water back into the main cell.
On 4/10/07, Christopher Gaughan <clgaughan68.gmail.com> wrote:
> here is my md.in file:
>
> &cntrl
> imin = 0, nmropt = 0,
>
> ntx = 1, irest = 0, ntrx = 1,
>
> ntxo = 1, ntpr = 10000,
> ntwr = 50,
> ntwx = 10000, ntwv = 0, ntwe = 0,
> ioutfm = 0, ntwprt = 0,
>
> ntf = 2, ntb = 1, dielc = 1.0,
> scnb = 2.0, scee = 1.2
>
> ibelly = 0, ntr = 0,
>
> nstlim = 1000000,
> dt = 0.002, pres0 = 1,
> temp0 = 300.00, tempi = 300.0, ig = 71277,
> ntt = 1,
> tautp = 1.0, vlimit = 0.0, ntp = 0,
>
> ntc = 2, tol = 0.00005,
>
> //
>
> However, I have erred in that the output from amber does not show that the
> volume is increasing (it shows no values for each time point). The problem
> arises when I view my trajectory in VMD 1.8.5- The waters, which initially
> start out as a box around my peptide, appear to to just expand out
> throughout the simulation.
>
> I am not sure if this is just a visualization problem inherent from the use
> of periodic boundary conditions (however I use the periodic box option in
> VMD) or whether the system is indeed expanding.
>
>
>
> On 4/9/07, David A. Case <case.scripps.edu> wrote:
> > On Mon, Apr 09, 2007, Christopher Gaughan wrote:
> > >
> > > I am running simulations in Amber 8 using N V T ensemble. However, when
> I
> > > track the volume during the MD runs I notice that it keeps increasing
> > > throughout the simulation.
> >
> >
> > We need more information. You are obviously not doing a constant volume
> > simulation. But all you have said so far is what you *intended* to do,
> not
> > what you actually did (i.e. not your input). Be sure to check the value
> of
> > ntp.
> >
> >
> > .....dac
> >
> >
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>
>
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Received on Wed Apr 11 2007 - 06:07:39 PDT
