<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear gmx's user,<BR>May I asked you some technicl Questions?<BR>Do you know how to make distance restraint in gromacs?<BR>what I did I have created file name "disre.itp" as shown below<BR>[ distance_restraints ]<BR>; ai aj type index type low up1 up2 fac<BR> 489 1133 1 1 1 0.25 0.35 0.40 1.0<BR> 489 1164 1 2 1 0.25 0.35 0.40 1.0<BR> 490 1127 1 3 1 0.25 0.35 0.40 1.0<BR> 490 1167 1 4 1 0.25 0.35 0.40 1.0<BR> <BR>in md.mdp
file:<BR> <BR>title = M2_amand in POPC<BR>cpp = /lib/cpp<BR>constraints = all-bonds<BR><FONT style="BACKGROUND-COLOR: #ffff00">define = -DDISRES</FONT><BR>integrator = md<BR>dt = 0.002 ; ps !<BR>nsteps = 500000 ; total 1000 ps = 1 ns !<BR>nstcomm =
1<BR>nstxout = 250<BR>nstvout = 1000<BR>nstfout = 0<BR>nstlog = 100<BR>nstenergy = 100<BR>nstlist = 10<BR>ns_type = grid<BR>rlist = 1.2<BR>coulombtype = PME<BR>rcoulomb =
1.2<BR>rvdw = 1.2<BR>pbc = xyz<BR>; Berendsen temperature coupling is on in two groups<BR>Tcoupl = berendsen<BR>tc-grps = Protein POPC SOL Cl<BR>tau_t = 0.1 0.1 0.1 0.1<BR>ref_t = 310 310 310 310<BR>; Energy monitoring<BR>energygrps = Protein POPC SOL
Cl<BR>; Isotropic pressure coupling is now on<BR>Pcoupl = berendsen<BR>Pcoupltype = isotropic<BR>tau_p = 1.0<BR>compressibility = 4.5e-5<BR>ref_p = 1.0<BR>; Generate velocites is off at 300 K.<BR>gen_vel = no<BR>gen_temp = 310.0<BR><FONT style="BACKGROUND-COLOR: #ffff00">disres = simple</FONT><BR><BR><BR>in topology.top file I added...<BR><BR>; Include distance restraint
file<BR>#ifdef DISRES<BR>#include "disre.itp"<BR>#endif<BR><BR>My questions are <BR>Q1:What is "column index" mean in disre.itp file? and how is it benefit?<BR>Q2:Where can I find in the output to make sure that my distances has already restrainted?<BR><BR> Thanks so much<BR> <BR>pathum<BR></td></tr></table><br>