[gmx-users] NVT ensemble

[Itamar Kass]

   Hi Farid, as much as I see from your attached mdp, you use NPT and 
not NVT.  Use pcoupl = no in order to use NVT.
    Cheers, Itamar.

fsaadedi at staffmail.ed.ac.uk wrote:
> Dear fellow users,
> 
> 
> I have been trying to equilibrate my DOPC bilayer using an NVT ensemble for
> 100ps.  Unfortunately the equilibration crashes after just 1.5ps.  It crashes
> because several bonds rotated more than 30 degrees.  I have tried contraining
> my bonds all-bonds, hbonds and none with no effect.  If anyone has any
> suggestions I would appreciate them.
> 
> Thank you for your time
> 
> Farid
> 
> 
> 
> I include my nvt.mdp file
> 
> 
> ; PREPROCESSING
> title                  = DOPC
> cpp                    = /lib/cpp
> include                = -I.
> 
> ; RUN CONTROL
> integrator             = md
> tinit                  = 0
> dt                     = 0.002
> nsteps                 = 50000
> nstcomm                = 1
> 
> ; LANGEVIN DYNAMICS
> 
> ; ENERGY MINIMIZATION
> ;emtol                  = 1000.0
> ;emstep                 = 0.01
> ;nstcgsteep             = 1000
> 
> ; SHELL MOLECULAR DYNAMICS
> 
> ; OUTPUT CONTROL
> nstxout                = 100 ; co-ordinates
> nstvout                = 0   ; velocities
> nstfout                = 0   ; forces
> nstlog                 = 0
> nstenergy              = 50
> nstxtcout              = 100
> 
> ; NEIGHBOR SEARCHING
> nstlist                = 10
> ns_type                = grid
> pbc                    = xyz
> rlist                  = 1.0
> 
> ; ELECTROSTATICS AND VDW
> coulombtype            = Cut-off
> rcoulomb               = 1.2      ; electrostatic cutoff in nm
> epsilon_r              = 100.0
> vdwtype                = Cut-off
> rvdw                   = 1.0      ; vdw/lj cutoff in nm
> dispcorr               = no
> 
> ; TEMPERATURE COUPLING
> tcoupl                 = nose-hoover
> tau_t                  = 0.01 0.01 0.01 0.01;0.1 0.1 0.1
> ref_t                  = 300 300 300 300
> tc_grps                = OLA OLB DPC SOL
> 
> ; PRESSURE COUPLING
> coupl                 = berendsen
> coupltype             = semi-isotropic
> ;tau_p                  = 5.0 5.0 5.0 ; was 5.0 5.0 5.0
> ;compressibility        = 4.5e-5 4.5e-5 4.5e-5
> ;ref_p                  = 1.0 1.0 1.0
> 
> ; SIMULATED ANNEALING
> annealing              = no
> zero_temp_time         = 100
> 
> ; VELOCITY GENERATION
> gen_vel                = yes
> gen_temp               = 300.0
> 
> 
> ;BONDS
> constraints            = hbonds ; none/all-bonds
> ;constraint_algorithm   = shake
> morse                  = no
> 
> ;Relative tolerance of shake
> shake-tol             = 0.0001
> 
> ; ENERGY GROUP EXCLUSIONS
> 
> ; NMR REFINEMENT
> 
> ; FREE ENERGY PERTUBATION
> free_energy             = no
> 
> ; NON-EQULIBRIUM MD
> 
> ; ELECTRIC FIELDS
> 
> 
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-- 


===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585194
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Web: http://munch.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
============================================
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