On Tue, Oct 30, 2007, Seongeun Yang wrote:
> I did again the test job with the following steps in amber9, loaded mdcrd in VMD,
> but I don't see any strange thing happen at all.
>
> > Can you try setting ntpr=1 and ntwx=1. Then take a look at the mdcrd file
> > that is created in something like VMD and see if you can see anything
> > strange happening to the structure. If you could also post the mdout file
> > it will be easier to try and work out what is going on.
>
> The topology file is made by:
> source leaprc.ff02pol.r1
> nma = sequence {ACE NME}
> solvateoct nma TIP3PBOX 8.0
> saveamberparmpol nma nma.top nma.crd
>
> With mdin:
> *************************************
> Heating to 100 K
> &cntrl
> imin = 0, ntx = 1,
> irest = 0, iwrap = 1,
> ntpr = 1, ntwe = 10,
> ntwr = 10, ntwx = 1,
> ntave = 500,
> ntf = 2, ntc = 2, ntb = 2,
> cut = 8.0, nsnb = 10,
> nstlim = 500, dt = 0.002,
> tempi = 5.0, temp0 = 100.0,
> ntt = 1, tautp = 1.0,
> ntp = 1, pres0 = 1.0, taup = 1.0,
> ipol = 1,
> /
> &ewald
> indmeth = 1,
> /
You need to equilibrate to 300 K before turning on constant pressure. That
is, try doing a constant volume simulation first. Also, what is your initial
density?
You may need to use a larger box, i.e. a bigger value than 8.0 in the
solvateoct command. Sander can run into the problems you see when trying to
simulate very small (by our standards!) systems.
...good luck...dac
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Received on Wed Oct 31 2007 - 06:07:59 PDT
