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