[gmx-users] Parrinello-Rahman and Simulated Annealing

[Baptiste Demoulin]

Dear Gromacs users,

I am trying to simulate a large systems embeded in a membrane (roughly
360,000 atoms). I would like to equilibrate it at 300K and 1 atm. To this
mean, I use simulated annealing to slowly warm up the system from 50 to
300K, under NPT conditions.

For the simulation, I use position restraints on the heavy atoms on the
protein, and stronger constraints on the metallic core, and LINCS to
constrain all the bonds, and 2 fs timestep.

My problem is that when I use Parrinello-Rahman barostat for the
simulation, I got LINCS warning concerning the restrained metallic core.
However, using Berendsen barostat for the same system, same input, seems to
work fine, (at least for the 200,900 steps I did until now). I thus tried
various modifications, such as changing the coupling tau_p, running first a
pure NVT at 50K for 2 ps, and then warming, but that did not work... Is
there an incompatibility between Parrinello-Rahman and simulated annealing
?

Here is my input:

define               = -DPOSRES -DPOSRES_CORE
integrator           = md
continuation         = no           ; first dynamics run
nsteps               = 1500000
dt                   = 0.002

nstcomm              = 1
comm-mode            = linear
comm-grps            = Protein_POPC SOL_NA_CL

pbc                  = xyz
nstlist              = 10
ns-type              = grid
rlist                = 1.0
rlistlong            = 1.6 ; the force on a particle which falls within
rlist and rlistlong is calculated during the pair list update and retained
during nslist steps
coulombtype          = pme
rcoulomb             = 1.0
vdwtype              = cut-off
rvdw                 = 1.4
DispCorr             = EnerPres

nstxtcout            = 10
nstxout              = 0
nstvout              = 0
nstfout              = 0
nstlog               = 10

constraints          = all-bonds
constraint-algorithm = lincs

tcoupl               = V-rescale
tc-grps              = Protein POPC SOL_NA_CL
tau_t                = 0.1  0.1  0.1
ref_t                = 300  300  300

pcoupl               = Parrinello-Rahman
pcoupltype           = semiisotropic
compressibility      = 4.5e-5 4.5e-5
tau_p                = 10.0
ref_p                = 1.0 1.0

refcoord_scaling     = com

gen_vel              = no
gen_temp             = 50
gen_seed             = -1

annealing            = single single single
annealing_npoints    = 2 2 2
annealing_time       = 0 2000 0 2000 0 2000
annealing_temp       = 50 300 50 300 50 300

Thank you very much for your help !

Baptiste