One of the possible cause may be the PBC and image issues.
Make sure that you have sufficient water around the solute and the
solute doesn't come out of box. You can superimpose/visualize the cuprit
frames
in VMD and see what's going wrong.
On Tue, Mar 10, 2015 at 3:24 PM, Anasuya Dighe <anasuya.mbu.iisc.ernet.in>
wrote:
>
> 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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--
*With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
TheoryDepartment of Physics IISc.,Bangalore India 560012*
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Received on Tue Mar 10 2015 - 03:30:03 PDT
