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

[Peter C. Lai]

On 2011-04-08 08:16:19AM -0500, Justin A. Lemkul wrote:
> 
> 
> Peter C. Lai wrote:
> > 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.
> 
> My recommendation was for the barostat, not the thermostat.
> 
> > 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?
> 
> No, that will make your life worse.  Just because the constraints fail doesn't 
> mean that you need to disable LINCS.
> 
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up

So basically, just keep running NVT until I can get NPT stabilized?
Thanks.
-- 
===============================================================
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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