[gmx-users] Re:Simulation Crash

[Justin A. Lemkul]

Kishore wrote:
> Dear Justin,
> I have used the same .mdp file you have used in your tutorial for 
> enzyme-ligand complex, I am pasting it here. My system consists of 10212 
> (enzyme+NADPH) atoms and 45000 water molecules.
> 

Try using the Berendsen barostat instead of P-R.  Some systems don't behave as
robustly and require a bit more gentle equilibration.  The P-R barostat allows
for much wider fluctuations in pressure in such cases that lead to instability.

Otherwise, you have to do a thorough analysis of the origin of the problem. 
Does your protein run alone?  What about the NADPH cofactor?  If one or both of 
these fails under the same conditions, you have a problem with your topology 
that is causing the instability.

-Justin

> title       = Protein-ligand complex NPT equilibration
> define      = -DPOSRES  ; position restrain the protein and ligand
> ; 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  = Protein NDPH
> ; Bond parameters
> continuation    = yes           ; 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       ; 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 is on
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = Protein_NDPH SOL_NA+    ; two coupling groups - more accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 300   300                     ; reference temperature, one 
> for each group, in K
> ; Pressure coupling is off
> pcoupl      = Parrinello-Rahman             ; pressure coupling is on 
> for NPT
> pcoupltype  = isotropic                     ; uniform scaling of box vectors
> tau_p       = 2.0                           ; time constant, in ps
> ref_p       = 1.0                           ; reference pressure, in bar
> compressibility = 4.5e-5                    ; isothermal compressibility 
> of water, bar^-1
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = no       ; assign velocities from Maxwell distribution
> 
> -- 
> KRISHNA KISHORE at IIT-MADRAS
> 

-- 
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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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