<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Thanks for the detailed explaination.</span></div><div><span></span> </div><div><span>Will you please explain the function of "-n index.ndx " in "grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr" with some specific examples?</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Acoot</div><div><br></div></span><div><br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="hr" contentEditable="false" readonly="true"></div> <b><span
style="font-weight: bold;">From:</span></b> Peter C. Lai <pcl@uab.edu><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Friday, 6 April 2012 2:24 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] further discussion on the mdrun -append function<br> </font> </div> <br>Sounds like there is a lanugage barrier?<br><br>Anyway, some cluster filesystems don't support append (e.g. lustre).<br><br>So I never use append.<br><br>I will use tpbconv -extend and -o to a *different* tpr file, then run<br><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><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>> > /-[no]append bool yes Append to previous output files when continuing <br>> > from checkpoint instead of adding the simulation art number to all <br>> > file names/<br>> > 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>> -- <br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br>-- <br>==================================================================<br>Peter C. Lai | University of Alabama-Birmingham<br>Programmer/Analyst | KAUL 752A<br>Genetics, Div. of Research | 705 South 20th Street<br><a href="mailto:pcl@uab.edu" ymailto="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>(205) 690-0808 |<br>==================================================================<br><br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
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