I'm a lowly undergrad who is trying to get to grips with amber and is having
a spot of difficulty.
I have been trying to simulate a DNA chain and Na+ counterions (added using
leap) by way of sander and the
implicit GB approx.
My problem is that on starting md to equilibrate the system the Na+ ions
quickly fly away from the DNA chain.
I have tried a couple of different protocols for equilibriation and
minimisation to no avail.
Is there some obvious reason why this is happening that I am overlooking?
It was suggested to me that it could be something to do with the Na+ GB
parameters.
Here is the input file for the first stage of equilibriation
&cntrl
imin = 0, nmropt = 1, ntb = 0,
igb=1, saltcon=0.0,
ntx=1, irest=0, ntrx=1, ntxo=1,
ntpr=100, ntwx=500, ntwv=0, ntwe=0,
ntc = 2, tol = 0.00001, ntf = 2,
ntt = 1, temp0 = 300.0, tempi = 100.0,
tautp = 0.2, vlimit = 25.0, ig = 71277,
heat = 0.0,
nstlim = 12500, dt = 0.002,
cut = 15.0,
ibelly = 0, ntr = 1,
&end
&wt
type='TEMP0', istep1=0, istep2=1000,
value1=10.0, value2=300.0,
&end
&wt
type='TEMP0', istep1=1000, istep2=12500,
value1=300.0, value2=300.0,
&endcp
&wt
type='END',
&end
&rst
iat=0,
&end
Hold the DNA - let the ions move
500.0
RES 1 24
END
END
Any help would be greatly appreciated,
Conn O'Rourke
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Received on Sun Jul 23 2006 - 06:07:07 PDT
