Vitaly Chaban wrote:
the equlibration file I used
title = cpeptid position restraining
cpp = /usr/bin/cpp
constraints = none
integrator = md
dt = 0.001 ; ps !
nsteps = 1000000 ; total 1.0 ps.
nstcomm = 1
nstxout = 10000
nstvout = 10000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = simple
comm_mode = none
coulombtype = cut-off
vdwtype = cut-off
rlist = 0.0
rcoulomb = 0.0
rvdw = 0.0
pbc = no
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = nose-hoover
tau_t = 0.1
tc-grps =system
ref_t = 298
; Pressure coupling is on
Pcoupl = NO ;Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 298.0
gen_seed = 173529
Is ther any thing wrong with my mdp files.
WHy they is so much change is cooridnates in the .pdb file.
Nilesh:
Set periodic conditions. This will restrict the coordinates to small numbers.
For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct to
obtain a gas-phase system. The system has clearly exploded. To diagnose, I
would suggest:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
-Justin
--
========================================
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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