[gmx-users] Fwd: How can i run my system successfully?

[bahareh khanoom]

Hi friends
I want to simulate a system that consists of 2 molecule on the graphite
surface. To generate " DRG.itp" for adsorbed molecule, I used PRODRG
server. I applied ffG43a1 for simulation this system. I did minimaization
energy without any problem, but when i run my system for nvt equilibration,
run exit. for example:

Step 79777, time 159.554 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.346309, max 1.958716 (between atoms 13 and 15)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     13     15   90.0    0.1000   0.2959      0.1000
Wrote pdb files with previous and current coordinates

so, what is the reason?


there are em.mdp and nvt.mdp that i used:

; em.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
;define          =-DPOSRES
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps = 50000    ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz  ; Periodic Boundary Conditions (yes/no)
freezegrps      = grap
freezedim       = Y Y Y


title       = NVT equilibration

;define         = -DPOSRES ; position restrain the protein

; Run parameters

integrator        = md ; leap-frog integrator

nsteps           = 7500000 ; 15000 ps= 15 ns

dt           = 0.002 ; 2 fs

; Output control

nstxout = 75000 ; save coordinates

nstvout = 75000 ; save velocities

nstxtcout       = 7500

nstenergy       = 7500 ; save energies every

nstlog = 7500 ; update log file every

; 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 cels

nstlist = 5 ; 10 fs

rlist = 1.4 ; short-range neighborlist cutoff (in nm)

rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)

rvdw = 1.4 ; short-range van der Waals cutoff (in nm)

freezegrps      = grap

freezedim       = Y Y Y

; Electrostatics

coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics

pme_order = 4 ; cubic interpolation

fourierspacing = 0.71 ; grid spacing for FFT

; Temperature coupling is on

tcoupl = V-rescale

tc-grps = DRG   grap ; three coupling groups - more accurate

tau_t = 0.1 0.1  ; time constant, in ps

ref_t = 400  400  ; reference temperature, one for each group, in K

; 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 = 400 ; temperature for Maxwell distribution

gen_seed = -1 ; generate a random seed

; COM motion removal

; These options remove motion of the protein/bilayer relative to the
solvent/ions

nstcomm = 1

comm-mode = Linear

comm-grps = DRG  grap

..........
Thanks in advance
Bahar