On 5/1/12 1:13 PM, niaz poorgholami wrote:
thank you Sir for your reply.below I provide you .mdp file:
title = UNK-ligand complex NVT equilibration
define = -DPOSRES -DPOSRES_LIG ; position restrain the UNK and LIG
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 1 ; save coordinates every 0.2 ps
nstvout = 1 ; save velocities every 0.2 ps
Your .trr files will be huge with these settings. I would only recommend
getting such output every step if your system were collapsing within just a few
steps, but not in this case. Though, if you have such output, watching the
trajectory (provided your workstation doesn't run out of memory) should point to
the problem.
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
energygrps = UNK LIG
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 0.9 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = UNK_LIG Water_and_ions ; two coupling groups -
more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
I see nothing particularly glaring with the .mdp file that would be causing a
problem. You also did not answer my question about EM, so it is still a
possibility that the system is insufficiently minimized, but that's just a guess
since I don't know.
Otherwise:
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
