[gmx-users] unable to equilibrate protein in membrane with NPT

[Peter C. Lai]

On 2011-04-08 08:02:14AM -0500, Justin A. Lemkul wrote:
> 
> 
> Peter C. Lai wrote:
> > Hello again
> > 
> > In my protein-membrane-water-ion system (inserted via g_membed) I have run 
> > a 1ns NVT equilibration with the protein restrained and now I am trying to 
> > equilibrate with NPT and LINCS/mdrun is crashing after about 5000 iterations.
> > 
> > Here is my NPT mdp file:
> > 
> > define                  =-DPOSRES
> > integrator               = md
> > ; Start time and timestep in ps
> > tinit                    = 0
> > dt                       = 0.002
> > nsteps                   = 500000
> > init_step                = 0
> > comm-mode                = Linear
> > nstcomm                  = 1
> > comm-grps                = Protein_POPC SOL_CL
> > 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
> > continuation    = yes
> > constraint_algorithm = lincs    ; holonomic constraints
> > constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> > lincs_iter      = 1             ; accuracy of LINCS
> > lincs_order     = 4             ; also related to accuracy
> > ns_type         = grid          ; search neighboring grid cells
> > nstlist         = 5             ; 10 fs
> > rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
> > rlistlong       = 1.4
> > rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
> > rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
> > vdwtype         = switch
> > rvdw_switch     = 0.8
> > coulombtype     = PME
> > pme_order       = 4             ; cubic interpolation
> > fourierspacing  = 0.16          ; grid spacing for FFT
> > tcoupl          = Nose-Hoover
> > tc-grps         = Protein POPC SOL_CL
> > tau-t                    = 0.5 0.5 0.5
> > ref-t                    = 300 300 300
> > gen-vel                  = no
> > pcoupl          = Parrinello-Rahman         ; Pressure coupling on in NPT
> > pcoupltype      = semiisotropic             ;
> > tau_p           = 5.0                           ; time constant, in ps
> > ref_p           = 1.01325 1.01325
> > compressibility = 4.5e-5        4.5e-5
> > 
> > Any suggestions?
> 
> Try using the Berendsen barostat.  P-R allows for wider oscillations that can 
> lead to instability in incompletely equilibrated systems.
> 
> -Justin
> 

Switching to V-rescale and tau_t to 0.1 0.1 0.1 also crashes.
LINCS is complaining about C-H interactions in both the mobile lipid chains
as well as atoms restrained by posre.itp

Maybe I will run without LINCS all-bond?
-- 
===============================================================
Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
(205) 690-0808               |
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