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.
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.
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
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. If not is there any way I can get velocities too when I create .rst file.
Thanks,
Nitin Sharma
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Tuesday, February 04, 2014 9:02 PM
To: amber.ambermd.org
Subject: Re: [AMBER] error in extending simulation from .rst file
On Tue, 2014-02-04 at 13:18 +0800, Nitin Sharma wrote:
> Dear amber users,
>
>
> I got error in extending simulation from a 50ns MD run restart file .
>
> ERROR: I could not understand line 11876
>
> -0.0694812 -0.0371947 -0.0775758 0.2710202 -0.5647205 -0.7658839
>
>
>
> Lines 11875, 11876 and 11877 are as follows:
>
> -309.6311297-120.7228754 -89.3867069-308.6193503-121.6398973
> -88.7337458
>
> -0.0694812 -0.0371947 -0.0775758 0.2710202 -0.5647205 -0.7658839
>
> 0.3368825 0.5317549 -0.2689358 0.3489688 -0.2916539 0.1023535
>
>
>
> However, on examination I found issues on following lines 11745 and
> 11746
>
> 298.5346412-355.8839842 34.9198195************
> 54.5942591-259.6477784
>
> ************ 55.0123119-258.9368236************
> 53.6829762-259.3702980
>
>
>
> So why is the error on line 11876 instead of lines 11745 and 11746?
I'm not sure why the error was reported for line 11876. I will look into this, but the real problem is on line 11745.
> As I am doing NPT simulation can someone tell me what each column of
> .rst file signifies as in another restart file I found last three
> columns missing from a partucluar line though no error was shown in
> exnteding simulation using that particular restart file
Restart files have the same format regardless of what type of simulation you are running. If a row has only 3 numbers, that means it is the coordinates or velocities of the last particle, and that your particle has an odd number of atoms.
The restart file format is fully described here:
http://ambermd.org/formats.html#restart
Basically, each number is a coordinate and the coordinates are arranged
as:
X1 Y1 Z1 X2 Y2 Z2
X3 Y3 Z3 X4 Y4 Z4
...
XN YN ZN
The last 6 numbers in the file are the box lengths and angles, respectively (if a periodic box exists).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 04 2014 - 10:30:02 PST
