[gmx-users] Frames problem

Mon Jun 16 08:24:21 CEST 2008

Hi All,
I have MD simulation which crashed and I combine the frames with trjconv. Now the problem is that when I do analysis like that of Solvent accessible surface area, it showed that the incomplete frame . I use the gmxcheck with the following result
d 1: 'Protein'
1695 out of 2854 atoms were classified as hydrophobic
Reading frame&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 20 time&nbsp; 400.000&nbsp;&nbsp; 
WARNING: Incomplete frame: nr 28 time 560

gcq#190: "That Was Cool" (Beavis and Butthead)

lalbadshah at linux:~/323&gt; gmxcheck -f md323.xtc -s1 md323.tpr -e md323.edr
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; :-)&nbsp; G&nbsp; R&nbsp; O&nbsp; M&nbsp; A&nbsp; C&nbsp; S&nbsp; (-:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Glycine aRginine prOline Methionine Alanine Cystine Serine

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; :-)&nbsp; VERSION 3.3.1&nbsp; (-:

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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; :-)&nbsp; gmxcheck&nbsp; (-:

Option&nbsp;&nbsp;&nbsp;&nbsp; Filename&nbsp; Type&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Description
------------------------------------------------------------
&nbsp; -f&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; md323.xtc&nbsp; Input, Opt!&nbsp; Generic trajectory: xtc trr trj gro g96 pdb
&nbsp;-f2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; traj.xtc&nbsp; Input, Opt.&nbsp; Generic trajectory: xtc trr trj gro g96 pdb
&nbsp;-s1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; md323.tpr&nbsp; Input, Opt!&nbsp; Generic run input: tpr tpb tpa xml
&nbsp;-s2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; top2.tpr&nbsp; Input, Opt.&nbsp; Generic run input: tpr tpb tpa xml
&nbsp; -c&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; topol.tpr&nbsp; Input, Opt.&nbsp; Structure+mass(db): tpr tpb tpa gro g96 pdb
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; xml
&nbsp; -e&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; md323.edr&nbsp; Input, Opt!&nbsp; Generic energy: edr ene
&nbsp;-e2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ener2.edr&nbsp; Input, Opt.&nbsp; Generic energy: edr ene
&nbsp; -n&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; index.ndx&nbsp; Input, Opt.&nbsp; Index file

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Option&nbsp;&nbsp; Type&nbsp; Value&nbsp; Description
------------------------------------------------------
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -[no]h&nbsp;&nbsp; bool&nbsp;&nbsp;&nbsp;&nbsp; no&nbsp; Print help info and quit
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -nice&nbsp;&nbsp;&nbsp; int&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp; Set the nicelevel
&nbsp;&nbsp;&nbsp;&nbsp; -vdwfac&nbsp;&nbsp; real&nbsp;&nbsp;&nbsp; 0.8&nbsp; Fraction of sum of VdW radii used as warning
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; cutoff
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -bonlo&nbsp;&nbsp; real&nbsp;&nbsp;&nbsp; 0.4&nbsp; Min. fract. of sum of VdW radii for bonded atoms
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -bonhi&nbsp;&nbsp; real&nbsp;&nbsp;&nbsp; 0.7&nbsp; Max. fract. of sum of VdW radii for bonded atoms
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -tol&nbsp;&nbsp; real&nbsp; 0.001&nbsp; Relative tolerance for comparing real values
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; defined as 2*(a-b)/(|a|+|b|)
&nbsp;&nbsp;&nbsp;&nbsp; -[no]ab&nbsp;&nbsp; bool&nbsp;&nbsp;&nbsp;&nbsp; no&nbsp; Compare the A and B topology from one file
&nbsp;&nbsp; -lastener string&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Last energy term to compare (if not given all are
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; tested). It makes sense to go up until the
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Pressure.

Reading file md323.tpr, VERSION 3.3.1 (single precision)
Checking file md323.xtc
Reading frame&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 time&nbsp;&nbsp;&nbsp; 0.000&nbsp;&nbsp; 
# Atoms&nbsp; 37959
Precision 0.001 (nm)
Reading frame&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 20 time&nbsp; 400.000&nbsp;&nbsp; 
WARNING: Incomplete frame: nr 28 time 560

Item&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; #frames Timestep (ps)
Step&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 28&nbsp;&nbsp;&nbsp; 20
Time&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 28&nbsp;&nbsp;&nbsp; 20
Lambda&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0
Coords&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 28&nbsp;&nbsp;&nbsp; 20
Velocities&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0
Forces&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0
Box&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 28&nbsp;&nbsp;&nbsp; 20
Checking energy file md323.edr

Opened md323.edr as single precision energy file
frame:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 (index&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0), t:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.000&nbsp; 
Last frame read 500 time 1000.000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 

Found 501 frames with a timestep of 2 ps.

gcq#58: "You Look Better Upside Down" (Throwing Muses)

Now what should I do? Please guide me.

SYED LAL BADSHAH 

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