Nilesh Dhumal wrote:
Hello
I am trying to constraints of a bond. I checked the distance using g_dist,
distance changes from 3.5 A to ~ 8.0A.
Can anyone tell why it changes.
Here I have pasted mdp file and itp file.
Maybe there's a bug in the interpretation of the constraints? The combination
of "constraints = none" + [constraints] directive should constrain the bond.
Have you tried simply defining a [bonds] directive and using "constraints =
all-bonds"?
-Justin
Nilesh
Solvent.itp
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
;1 3 yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_997 PA 0 100.0000 1.000 A 0.40000e-01 0.82890e-01
opls_998 NE 0 100.0000 -1.000 A 0.40000e-01 0.82890e-01
[ bondtypes ]
; i j func b0 kb
PA NE 1 0.350000 000000
[ moleculetype ]
; name nrexcl
ABC 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 opls_997 1 ABC PA 1 1.0000 100.0000
2 opls_998 1 ABC NE 1 -1.0000 100.000
[ constraints ]
1 2 1 0.35000
pr.mdp
title = cpeptid position restraining
cpp = /usr/bin/cpp
constraints = none
integrator = md
dt = 0.001 ; ps !
nsteps = 250000 ; total 1.0 ps.
nstcomm = 1
nstxout = 10
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
vdwtype = cut-off
rcoulomb = 1.0
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
constraint-algorithm = SHAKE
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
tc-grps =system
ref_t = 400
; Pressure coupling is not on
Pcoupl = no
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 400.0
gen_seed = 173529
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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