Nilesh Dhumal wrote:
Its oscillate between +/- 3-4 A.
If I freeze the distance by using freeze groups and dim in mdp file. It
works perfectly for NVT simulations. It oscillate for NPT simulation.
I don't know if there have been any changes (I don't see anything in the
revision history), but as far as I know, freezing is incompatible with NPT
ensembles due to the inability to scale the frozen coordinates.
-Justin
Nilesh
On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
constraints = all-bonds is working. I have solvent molecule for which I
don't want constraints on them. I can't use constraints = all-bonds
for simulation.
So you used g_dist to determine the distances with the setup shown below,
but did you correct for PBC effects? Is there a systematic increase in
the distance between the two particles, or does it oscillate?
-Justin
Nilesh
On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote:
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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========================================
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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--
========================================
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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