*hi! I am attempting to run a distance & position restrained simulation in water. The **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 Thanks Jayant James * *TOP FILE*
; Include Position restraint file #ifdef POSRES ;include "posre.itp" #endif ;include"disres.itp" ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_D 1 SOL 70360 NA+ 14 *em.mdp *; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /usr/bin/cpp define = -DFLEXIBLE -DPOSRES constraints = none integrator = steep nsteps = 100000 disre = simple ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no *pr.mdp* title = Nterm of TnC free (1-19) and TnT fully constrained cpp = /usr/bin/cpp define = -DPOSRES -DFLEXIBLE constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100000 ; total 200 ps. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 disres = simple ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-Protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 *disres.itp *[ distance_restraints ]* *; ai aj type index type' low up1 up2 fac 973 926 1 1 1 20.7 21.7 30.5 1.0 842 926 1 1 1 16.3 17.3 20.9 1.0 429 926 1 1 1 40.15 41.15 52.85 1.0 973 1079 1 1 1 39.45 30.45 48.75 1.0 842 1079 1 1 1 21.85 22.85 33.55 1.0 429 1079 1 1 1 40 42 65.3 1.0 973 1148 1 1 1 38 39 61.2 1.0 842 1148 1 1 1 32 33.75 53.7 1.0 429 1148 1 1 1 52 54.9 72.9 1.0 973 1216 1 1 1 42 46.35 69.25 1.0 842 1216 1 1 1 43 43.85 64.55 1.0 429 1216 1 1 1 57 59.8 81.6 1.0 973 1284 1 1 1 48 50.05 76.35 1.0 842 1284 1 1 1 45 47.4 76.9 1.0 429 1284 1 1 1 55 58.95 94.45 1.0 * posres.itp* [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 10 1 1000 1000 1000 11 1 1000 1000 1000 12 1 1000 1000 1000 14 1 1000 1000 1000 15 1 1000 1000 1000 . . . . . . . . . . . . -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164
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