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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Received on Wed Apr 11 2007 - 06:07:39 PDT
