On 7/10/13 3:13 AM, ashish24294 wrote:
I changed the cut-offs as follows, still isn't helping. I tried restraining
the urea which also didn't work. I have attached the topology as well.
topolurea.top
<http://gromacs.5086.x6.nabble.com/file/n5009723/topolurea.top>
The urea.itp looks suspicious to me - there are no angles defined. There is no
citation for the parameters in the .itp, so it's hard to validate where they
came from. In any case, given the frequency of output you have specified below,
it should be very useful to watch the trajectory to see what is going wrong.
Right around 25 ps, you have large oscillations in LJ(SR) and the temperature,
indicating to me that there is some really nasty geometry emerging that is
causing velocities to go haywire and the thermostat can't keep up. Then you get
the crash.
-Justin
*The nvt.mdp*
title = UREA_in_WATER NVT equillibration
;define = -DPOSRES_UREA
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
energygrps = URE
; 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 = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = URE_Water ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each
group, in K
; Pressure coupling
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
Using the above nvt.mdp file i got the attached nvt.log nvt.log
<http://gromacs.5086.x6.nabble.com/file/n5009723/nvt.log>
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--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Associate
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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