<i>hi!<br>I am attempting to run a distance & position restrained simulation in water. The </i><i>distance and position restraining files are called from the *.top file as posres.itp and disres.itp. After a 200ps run I do not see the distance nor position restraining kicking in. I am not sure if I have specified every thing correctly. I have pasted essential parts of the topology file, em.mdp, pr.mdp, disres.itp and posres.itp. Awaiting your feedback<br>
Thanks<br>Jayant James<br></i><br><u><b>TOP FILE</b></u><br><br>; Include Position restraint file<br>#ifdef POSRES<br>;include "posre.itp"<br>#endif<br><br>;include"disres.itp"<br><br>; Include water topology<br>
#include "spc.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>
#endif<br><br>; Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>; Name<br>Protein<br><br>[ molecules ]<br>; Compound #mols<br>Protein_D 1<br>SOL 70360<br>NA+ 14<br>
<br><br><b><u>em.mdp<br><br clear="all"></u></b>;<br>; User spoel (236)<br>; Wed Nov 3 17:12:44 1993<br>; Input file<br>;<br>cpp = /usr/bin/cpp<br>define = -DFLEXIBLE -DPOSRES<br>
constraints = none<br>integrator = steep<br>nsteps = 100000<br>disre = simple<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 2000<br>emstep = 0.01<br>
<br>nstcomm = 1<br>ns_type = grid<br>rlist = 1<br>rcoulomb = 1.0<br>rvdw = 1.0<br>Tcoupl = no<br>Pcoupl = no<br>gen_vel = no<br>
<br><u><b>pr.mdp</b></u><br><br>title = Nterm of TnC free (1-19) and TnT fully constrained<br>cpp = /usr/bin/cpp<br>define = -DPOSRES -DFLEXIBLE<br>constraints = all-bonds<br>
integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 100000 ; total 200 ps.<br>nstcomm = 1<br>nstxout = 5000<br>nstvout = 5000<br>nstfout = 5000<br>
nstlog = 5000<br>nstenergy = 5000<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>rcoulomb = 1.0<br>rvdw = 1.0<br>disres = simple<br>
; Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tc-grps = Protein Non-Protein<br>tau_t = 0.1 0.1<br>ref_t = 300 300<br>
; Energy monitoring<br>energygrps = Protein Non-Protein<br>; Pressure coupling is not on<br>Pcoupl = no<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>
; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br><u><b>disres.itp<br><br></b></u>[ distance_restraints ]<u><b><br></b></u>; ai aj type index type' low up1 up2 fac<br>
973 926 1 1 1 20.7 21.7 30.5 1.0<br> 842 926 1 1 1 16.3 17.3 20.9 1.0<br> 429 926 1 1 1 40.15 41.15 52.85 1.0<br>
973 1079 1 1 1 39.45 30.45 48.75 1.0<br> 842 1079 1 1 1 21.85 22.85 33.55 1.0<br> 429 1079 1 1 1 40 42 65.3 1.0<br>
973 1148 1 1 1 38 39 61.2 1.0<br> 842 1148 1 1 1 32 33.75 53.7 1.0<br> 429 1148 1 1 1 52 54.9 72.9 1.0<br>
973 1216 1 1 1 42 46.35 69.25 1.0<br> 842 1216 1 1 1 43 43.85 64.55 1.0<br> 429 1216 1 1 1 57 59.8 81.6 1.0<br>
973 1284 1 1 1 48 50.05 76.35 1.0<br> 842 1284 1 1 1 45 47.4 76.9 1.0<br> 429 1284 1 1 1 55 58.95 94.45 1.0<br>
<u><b><br></b><b>posres.itp</b></u><br><br>[ position_restraints ]<br>; atom type fx fy fz<br> 1 1 1000 1000 1000<br> 5 1 1000 1000 1000<br> 6 1 1000 1000 1000<br> 7 1 1000 1000 1000<br>
8 1 1000 1000 1000<br> 9 1 1000 1000 1000<br> 10 1 1000 1000 1000<br> 11 1 1000 1000 1000<br> 12 1 1000 1000 1000<br> 14 1 1000 1000 1000<br> 15 1 1000 1000 1000<br>
. . <br>. .<br>. .<br>. .<br>. .<br>. .<br><br><br><br><br>-- <br>Jayasundar Jayant James<br><br><a href="http://www.chick.com/reading/tracts/0096/0096_01.asp">www.chick.com/reading/tracts/0096/0096_01.asp</a>) <br>
Residence -24935864, cell-9841042164