Hi, I was running a DPPC system with 128 DPPC and 3655 water molecules in 16 CPU with -shuffle -sort option. But I am unable to continue the job in parallel. I read a lots of posts in mailing list, but could not understand the proper way, as I don't know the script languages. So whatever is mentioned in the list, I could not use those properly. Can anyone explain the procedure in a simpler way such that a poor scripter like me can follow? The details what I have done are as follows
1.grompp -f grompp.mdp -c input1.gro -p dppc.top -n index.ndx -np 16 -shuffle -sort 2./opt/lam/gnu/bin/mpirun c0-15 /home/ananya/gromacs/bin/mdrun_mpi -v -nice 0 then I get the output as, say, topol1.tpr, traj1.trr, confout1.gro, ener1.edr, deshuf1.ndx ------------------------------------------------------------------------------------------ If I follow the mail as I am going to copy here, I can follow upto step 3. In step 4, what is shuffled top file? If I undersant correctly, I have to get that from my original top file, which is dppc.top for me using that awk script. But how to use that I did not understand. Any suggestion is highly appreciated. Thanking you, Regards, Ananya. -------------------------------------------------------------------------------------------------------------------------------------- Hi, Make it simple, to use grompp for exact continuation, you need to have 1. mdp file with "gen_vel = no", "unconstrained-start = yes", 2. shuffled trr (original output) 3. shuffled edr (original output) 4. shuffled top (use below awk script to parse the output from your previous grompp output which contains the shuffled table) replace the [ molecules ] section in your top with the output of this script. BEGIN { begin=0 } { if ($1=="Moltype") { begin=1 for (i=0;i<NF-2;i++) { moltype[i] = $(i+2) } molnum=NF-2 } else { if (begin==1) { if($1=="CPU") { for (i=0;i<molnum;i++) { if ($(3+i)==0) continue printf("%s\t%d\n", moltype[i], $(3+i)) } } else begin=0 } } } 5. don't supply -shuffle -sort again to grompp. Last, the grompp command line like $pp -np ${ncpu} -c ${type1}-shuf.gro -t ${type1}-shuf.trr -e ${type1} \ -p ${dirp}/${type} -n ${dirp}/${type} -f ${mdp_file1} \ -o ${type2}.tpr -po ${type2}-o _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php