[gmx-users] LINCS WARNING - Protein-Membrane-system

[Shima Arasteh]

 If I tell you that I changed the constraints and now the NVT is running, would that be ok? However I don't know the scientific reason of this incident!

But I bring you the EM.mdp as follow:
define         = -DSTRONG_POSRES
integrator    = steep        ; Algorithm (steep = steepest descent minimization)
emtol        = 100.0      ; Stop minimization when the maximum force < 100.0 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


And the NVT.mdp as follow (after change of all-bond constraint to h-bond):
title        = NVT equilibration for dimer-POPC   -  CHARMM36
define        = -DPOSRES    ; Protein is position restrained (uses the posres.itp file information)
; Parameters describing the details of the NVT simulation protocol
integrator    = md        ; Algorithm ("md" = molecular dynamics [leap-frog integrator]; "md-vv" = md using velocity verlet; sd = stochastic dynamics)
dt        = 0.002        ; Time-step (ps)
nsteps        = 50000    ; Number of steps to run (0.002 * 50000 = 100 ps)

; Parameters controlling output writing
nstxout        = 1        ; Write coordinates to output .trr file every 2 ps
nstvout        = 1000        ; Write velocities to output .trr file every 2 ps
nstenergy    = 1000        ; Write energies to output .edr file every 2 ps
nstlog        = 1000        ; Write output to .log file every 2 ps
; Parameters describing neighbors searching and details about interaction calculations
ns_type        = grid        ; Neighbor list search method (simple, grid)
nstlist        = 5        ; Neighbor list update frequency (after every given number of steps)
rlist        = 1.2        ; Neighbor list search cut-off distance (nm)
rlistlong       = 1.4
rcoulomb    = 1.2        ; Short-range Coulombic interactions cut-off distance (nm)
rvdw        = 1.2        ; Short-range van der Waals cutoff distance (nm)
pbc        = xyz        ; Direction in which to use Perodic Boundary Conditions (xyz, xy, no)
vdwtype         = switch
rvdw_switch     = 0.8
; Parameters for treating bonded interactions
continuation    = no        ; Whether a fresh start or a continuation from a previous run (yes/no)
constraint_algorithm = LINCS    ; Constraint algorithm (LINCS / SHAKE)
constraints    = h-bonds      ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles)
lincs_iter    = 1        ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy)
lincs_order    = 4        ; Highest order in the expansion of the constraint coupling matrix (related to accuracy)

; Parameters for treating electrostatic interactions
coulombtype    = PME        ; Long range electrostatic interactions treatment (cut-off, Ewald, PME)
pme_order    = 4        ; Interpolation order for PME (cubic interpolation is represented by 4)
fourierspacing    = 0.16        ; Maximum grid spacing for FFT grid using PME (nm)

; Temperature coupling parameters
tcoupl        = v-rescale            ; Modified Berendsen thermostat using velocity rescaling
tc-grps        = Protein POPC    SOL_CL    ; Define groups to be coupled separately to temperature bath
tau_t        = 0.1    0.1    0.1        ; Group-wise coupling time constant (ps)
ref_t        = 310     310    310        ; Group-wise reference temperature (K)

; Pressure coupling parameters
pcoupl        = no         ; Under NVT conditions pressure coupling is not done

; Miscellaneous control parameters
; Dispersion correction
DispCorr    = EnerPres    ; Dispersion corrections for Energy and Pressure for vdW cut-off
; Initial Velocity Generation
gen_vel        = yes        ; Generate velocities from Maxwell distribution at given temperature
gen_temp    = 310        ; Specific temperature for Maxwell distribution (K)
gen_seed    = -1        ; Use random seed for velocity generation (integer; -1 means seed is calculated from the process ID number)
; Centre of mass (COM) motion removal relative to the specified groups
nstcomm        = 1            ; COM removal frequency (steps)
comm_mode    = Linear        ; Remove COM translation (linear / angular / no)
comm_grps    = Protein_POPC SOL_CL    ; COM removal relative to the specified groups


Any suggestions please?


Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Tuesday, January 1, 2013 7:17 PM
Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system



On 1/1/13 10:41 AM, Shima Arasteh wrote:
> Thanks.
> I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was  "constraints  = h-bonds ", however it was "constraints = all-bonds" for POPC/PROTEIN/WATER system.
> 
> You say insufficient minimization, I don't think so........ . I got a sensible potential energy as follow:
> Potential Energy  = -1.2414742e+06
> Maximum force     =  9.8055229e+01 on atom 4719
> Norm of force     =  3.4904923e+00
> Then what's wrong with the EM?
> 

Please post a complete .mdp file for both the EM and NVT processes.  Without that information, it's pure guesswork.

-Justin

-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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