On Wed, 2014-02-05 at 02:07 +0800, Nitin Sharma wrote:
> Jason thanks for the reply
>
> As my system has 24235 atoms and the first coordinate starts from
> third lines the coordinate of last atom was found on line 12120.
>
> The last six numbers present in line 24239 represents the periodic
> box.
>
> So the number from line 12121 to 24238 represent velocities?
>
> And in summary I can say
> X1 Y1 Z1 X2 Y2 Z2
> X3 Y3 Z3 X4 Y4 Z4
> ...
> XN YN ZN
> VX1 VY1 VZ1 VX2 VY2 V Z2
> VX3 VY3 V Z3 VX4 VY4 VZ4
> ...
> VXN VYN VZN
> PbL1 PbL2 PbL3 PbA1 PbA2 PbA3
>
> Where VX is velocity of X coordinate and so on and PbL is periodic box
> length and PbA is periodic box angle.
Yes.
> I created restart file from the .mdrcd file using following process
> trajin 5md.mdcrd
> trajout 5md_restart.rst restart
>
> I observed that velocities were missing and coordinated varied from
> 5th decimal place onwards.
The mdcrd files do not contain velocity information (unless you set ntwv
< 0 and you are using NetCDF). Also, NetCDF stores coordinates in
single precision, which may lead to the differences you noticed in some
coordinates.
>
> Coordinates from original .rst file with error
> 298.4016523-355.0298115 35.3308363 299.2754399-354.7625831 35.6159961
> 298.5346412-355.8839842 34.9198195************ 54.5942591-259.6477784
> ************ 55.0123119-258.9368236************ 53.6829762-259.3702980
> 273.4109890 85.0360253 223.0180692 273.1682910 84.2481699 222.5316399
>
> Coordinates from .rst file created from the trajectory
> 298.4016418-355.0298157 35.3308372 299.2754517-354.7625732 35.6159973
> 298.5346375-355.8839722 34.9198189-1051.959228 54.5942574-259.6477661
> -1051.473388 55.0123138-258.9368286-1052.052978 53.6829758-259.3703003
> 273.4109802 85.0360260 223.0180664 273.1683044 84.2481689 222.5316467
I don't know if these new coordinates will work or not, but you can try
it. I would suggest using "iwrap=1" (or imaging with cpptraj before
creating this restart file) to avoid getting values <= -1000 or >=10000.
The fixed format that the restart file uses cannot handle such large
numbers. Alternatively, use the NetCDF restart file (ntxo=2 in
sander/pmemd).
>
> Will it be advisable if I take velocities from the original file in
> the one created from the trajectory file OR I can take coordinates for
> the atoms with missing values from the one created.
I think that should be fine.
> If not is there any way I can get velocities too when I create .rst
> file.
No.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 04 2014 - 10:30:03 PST
