<br><br><div class="gmail_quote">On Fri, Apr 6, 2012 at 12:24 AM, Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Sounds like there is a lanugage barrier?<br>
<br>
Anyway, some cluster filesystems don't support append (e.g. lustre).<br></blockquote><div><br></div><div>I often use append on lustre. No problem. Why do you think it doesn't work? </div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
So I never use append.<br>
<br>
I will use tpbconv -extend and -o to a *different* tpr file, then run<br></blockquote><div><br></div><div>Even if you don't want to use append you don't need to use tpbconv. You can run mdrun -wth -noappend with the total you want for nsteps. mdrun automatically creates files called e.g. traj.part0002.trr.</div>
<div><br></div><div>Roland</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
mdrun -deffnm new_extended which generates everything with the new_extended<br>
filename prefix. Then I can trjcat or enerconv to concatenate everything<br>
together before running the analysis.<br>
<br>
Detailed Example:<br>
<br>
md.mdp is configured for 1ns of simulation time<br>
<br>
grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr<br>
<br>
mdrun -deffnm md-1ns<br>
<br>
-deffnm write out all files starting with this parameter: md-1ns.trr,<br>
md-1ns.edr, md-1ns.log, etc.<br>
<br>
Note: do not use a file extension for -deffnm or else it will put that in<br>
the resulting filenames. If you use -deffnm md-1ns.tpr it will write out<br>
files called md-1ns.tpr.trr md-1ns.tpr.edr etc.<br>
<br>
...<br>
<br>
tpbconv -s md-1ns.tpr -extend 2000 -o md-1ns-to-3ns.tpr<br>
<br>
mdrun -deffnm md-1ns-to-3ns -cpi md-1ns.cpt<br>
<br>
If you do not use -cpi here, your simulation will restart from 0, and will<br>
be written to files beginning with "md-1ns-to-3ns"<br>
<br>
The -cpi makes it continue from md-1ns.cpt but because of *different<br>
filenames*, it will not append, and therefore will write new files<br>
starting at 1ns.<br>
<br>
...<br>
<br>
trjcat -f md-1ns.trr md-1ns-to-3ns.trr -o md-to-3ns.xtc<br>
eneconv -f md-1ns.edr md-1ns-to-3ns.edr -o md-to-3ns.edr<br>
<br>
g_energy -f md-to-3ns.edr -o total-energy.xvg will give you a continuous<br>
.xvg from 0 to 3ns...<br>
<br>
If you only analysed md-1ns-to-3ns.trr/.edr then your curves will only start<br>
from 1ns onwards.<br>
<br>
Thus the trick is: use different file prefixes all the time and do not use<br>
append. It is the least confusing workflow to use.<br>
<div><br>
On 2012-04-06 01:56:18PM +1000, Mark Abraham wrote:<br>
> On 6/04/2012 1:41 PM, Acoot Brett wrote:<br>
> > Dear All,<br>
> > Frim mdrun -h, I got the following message:<br>
</div>> > /-[no]append bool yes Append to previous output files when continuing<br>
<div>> > from checkpoint instead of adding the simulation art number to all<br>
</div>> > file names/<br>
<div>> > Thus there is the possibility that the series xvg curves can never<br>
> > starts from 0 ns. Do you agree,<br>
><br>
> No. If you have your initial trajectory, then I told you about both the<br>
> available workflows yesterday. I'm going to stop repeating myself.<br>
><br>
> Mark<br>
<br>
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Peter C. Lai | University of Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br><a href="tel:865-241-1537" value="+18652411537" target="_blank">865-241-1537</a>, ORNL PO BOX 2008 MS6309<br>