Miguel Quiliano Meza wrote:
Dear Justin.
Thank you for you answer.
But, the case I wrote, it was an ideally case. To help anyone in the
forum at the same time.
As soon as I have read your answer I tried. In my case my simulations were:
First simulation: 0.4ns
Second : 1ns
Third: 2ns
Fourth: 10ns
----------------------
Total = 13.4ns
So I planned to do an RMSD plot of 0-13.4ns. As I said before, each
simulation is the continuation of the previous, obviously to do this I
used checkpoint files for each simulation and the same MD.mdp, only
changed the time of simulation.
I did:
trajcat -f md_0_4ns_noPBC.xtc md_1ns_noPBC.xtc md_2ns_noPBC.xtc
md_10ns_noPBC.xtc -o TOTAL_13_4ns_noPBC.xtc
Then for curiosity I did > ls -lh
rw-r--r-- 1 willy bioinfo 368M 2011-06-01 13:10 md_0_4_noPBC.xtc
-rw-r--r-- 1 willy bioinfo 917M 2011-06-01 13:12 md_1ns_noPBC.xtc
-rw-r--r-- 1 willy bioinfo 917M 2011-06-01 13:13 md_2ns_noPBC.xtc
-rw-r--r-- 1 willy bioinfo 9.0G 2011-06-01 13:17 md_10ns_noPDB.xtc
-rw-r--r-- 1 willy bioinfo 9.0G 2011-06-01 15:44 TOTAL_13_4ns_noPBC.xtc
Surprisingly the file "TOTAL_13_4ns_noPBC.xtc" had the same size of the
file "md_10ns_noPDB.xtc", is it normal?
No, it's not. But I don't know what you really typed. For one, the command is
not "trajcat," it's "trjcat." As well, the file name is "md_10ns_noPDB.xtc,"
apparently, not "md_10_noPBC.xtc." Please always copy and paste your commands
from the terminal; due to the filename inconsistency I can't tell where the
error is. Please post:
1. The real command, copied and pasted
2. The output of gmxcheck on each of the .xtc files
Another problem is that you haven't used -settime (or maybe you did, but your
command might not be transcribed properly), which would cause overlapping frames
to over-write one another.
Continue with the process, then:
>g_rms -s molecule_sol_ion_MD_0_4ns.tpr -f TOTAL_13_4ns_noPDB.xtc -o
rmsd_13_4ns_molecule.xvg -tu ns
I open the .XVG as a simple .txt and I noticed that the time only reach
10ns or 10000ps. Why not 13.4ns?
I would be very grateful If you can tell me what is happening.
I can't tell yet. If you've omitted -settime, then you're overwriting frames
and ending up with fragmented input. If you're not specifying the correct
filenames, you might be skipping times.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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