AMBER Archive (2009)

Subject: [AMBER] rmsd

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Fri Nov 20 2009 - 10:32:24 CST

Hi,

I need help understanding an RMSd plot.

after a dynamics run i use the following ptraj scripts

strip
{trajin MD.mdcrd
trajout MDnw.mdcrd
center:1-126
image familiar
strip :WAT*
go
}

and
rms
{trajin MDnw.mdcrd
trajin MD1nw.mdcrd
reference 1.rst
rms reference mass out lin.dat ':1' time 0.2
rms reference mass out SUR.dat ':2' time 0.2
rms reference mass out APT.dat ':3' time 0.2
rms reference mass out DNA.dat ':4-22' time 0.2
rms reference out DNAa.dat ':4-22@%CA' time 0.2
rms reference mass out olig1.dat ':23-74' time 0.2
rms reference mass out olig2.dat ':75-126' time 0.2
rms reference out Naion.dat ':231-249' time 0.2
}

the dynamics run is as follows
Molecular Dynamics for 2ns - only Surface atoms are fixed

  &cntrl
    imin = 0,
    irest = 1,
    ntx = 5,
    ntb = 2,
    pres0 = 1.0,
    ntp = 2,
    taup = 5.0,
    cut = 8.0,
    ntr = 1,
    ntc = 2,
    ntf = 2,
    temp0 = 300.0,
    ntt = 1,
    iwrap = 1,
    nstlim = 1000000, dt = 0.002
    ntpr = 5000, ntwx = 5000, ntwr = 50000
  /
Hold Surface fixed
20.0
RES 2 2
END
END

shouldn't the plot increase in the beginning and then level off, i don't
understand why would RMSd oscillate like this. i hope i made an error
with my calculations and this is not an indication of a problem with the
simulation.

Many thanks,
Taufik


rmsd.jpg

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