[AMBER] Sudden RMSD blow-up in trajectory analysis

From: Anasuya Dighe <anasuya.mbu.iisc.ernet.in>
Date: Tue, 10 Mar 2015 15:24:17 +0530 (IST)

Dear Amber Users,
  I have run a 100ns MD of a protein. Following is the .in file i was using the
run the simulation
----
100ps MD
 &cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  cut = 10.0, ntr = 0,
  ntc = 2, ntf = 2,ig = -1,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 50000, dt = 0.002,
  ntpr = 100, ntwx = 100, ntwr = 1000
 /
----
However, when I am analysing the trajectories, I am facing some issues.
 (1) After completion of the production run of 100ns, I am using the first frame
of the production dynamics to obtain a RMSD using cpptraj. The following are
the commands that I am using for the same.
---RMSD.in---
trajin ./1abc-md1.crd
.
.
.
trajin ./1abc-md1000.crd
strip :WAT
center :1-325 mass origin
image origin center familiar
rms first out rms-test.dat :1-325.CA
atomicfluct out per-res-fluct.dat :1-325 byres
go
------------
The resulting output file is showing a blowup of rmsd to 19.6556 Angstrom for
almost 19 frames in the simulation around the 80th ns.
(please see data below) The rest of the RMSD data, does not show any such
drastic deviations. It stays in the 2.0 to 3.0 Angstrom range.
----RMSD DATA---
  399601       2.7011
  399602       2.6962
  399603       2.7055
  399604       2.6971
  399605       2.7137
  399606       2.7178
  399607       2.6781
  399608       2.6682
  399609       2.6534
  399610       2.6402
  399611      19.6556 <---
  399612      19.6556 <---
  399613      19.6556 <---
  399614      19.6556 <---
  399615      19.6556 <---
  399616      19.6556 <---
  399617      19.6556 <---
  399618      19.6556 <---
  399619      19.6556 <---
  399620      19.6556 <---
  399621      19.6556 <---
  399622      19.6556 <---
  399623      19.6556 <---
  399624      19.6556 <---
  399625      19.6556 <---
  399626      19.6556 <---
  399627      19.6556 <---
  399628      19.6556 <---
  399629      19.6556 <---
  399630       2.5816
  399631       2.5835
  399632       2.5920
  399633       2.5742
  399634       2.5583
  399635       2.5812
------
What could be happening here ? Why this drastic difference in the RMSD ? What
was peculiar is, nowhere else in the simulation was there such a leap in RMSD.
(2) When I traced back the frames to the corresponding MD simulation, I tried
visualizing the relevant mdcrd file in VMD. This produced visualization of only
the first nine frames i.e from frame number 399601-399610. At the next step, VMD
crashed. Why is this happening ?
(3) Next to probe further, I tried to see whether there were some issues with
the protein structure in these frames. When I tried using cpptraj for the
extraction of PDB files for these frames, I got the following error message :
----------
1uh7-wat-md801.crd (1-500, 1)
 0% Warning: For PDB, box coords for first frame only will be written to CRYST1.
Warning: Frame 11 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 12 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 13 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 14 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 15 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 16 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 17 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 18 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 19 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 20 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 21 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 22 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 23 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 24 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 25 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 26 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 27 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 28 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 29 coords 1 & 2 overlap at origin; may be corrupt.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----------
Are these two issues related ?
What seems to be going wrong here in the simulation? What can i do to rectify
this error?
Please help.
Regards,
Anasuya Dighe
Indian Institute of Science,
Bangalore,
INDIA
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Received on Tue Mar 10 2015 - 03:00:02 PDT
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