AMBER Archive (2008)

Subject: AMBER: B-factor calculation from data with different write frequencies

From: Sally Pias (sallypias_at_gmail.com)
Date: Mon May 26 2008 - 23:19:42 CDT

Hello,

I wondered if anyone could help me with a Sander data analysis
problem. I naively changed write frequency in the middle of a lengthy
simulation, using ntwx = 100 for the first 2.5 ns and ntwx = 250 for
another 5 ns. Having done this, I am experiencing a problem combining
the data from the two segments for analysis with ptraj. Specifically,
I would like to calculate B-factors (and will later tackle NMR order
parameters). I have not found a way to specify in ptraj different
write frequencies for different .mdcrd files read in. Thus, ptraj
"sees" the timesteps from each data set as equivalent. Is there an
easy way to handle this problem, without rerunning the MD simulations?

I have thought about creating a new trajectory file by generating less
frequent snapshots from the first 2.5 ns (run with ntwx = 100).
However, I don't know how I would generate such a file with an
"apparent" write frequency of 250 (because the ntwx = 100 file lacks
data for the "in between" time steps).

In case they are helpful, I am including below example input files
used to generate the two different segments of the trajectory.

Thanks in advance for any help.

Sally Pias

====
&cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  cut = 10, ntr = 0,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 500000, dt = 0.002,
  ntpr = 100, ntwx = 100, ntwr = 1000,
  nmropt = 1,
/
&wt type = 'END'
/
LISTOUT = restraint_violations.out
DISANG = bmrb_noe_list.ambrst
====
====
&cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  cut = 10, ntr = 0,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 1250000, dt = 0.002,
  ntpr = 250, ntwx = 250, ntwr = 10000,
  nmropt = 1,
/
&wt type = 'END'
/
LISTOUT = restraint_violations.out
DISANG = bmrb_noe_list.ambrst
====
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