Hi gromacs users:
Using amber/charmm force field we simulated a solvated protein system
at different temperature(300,250 and 200K).
I used TIP5P water model and applied NVT ensemble . We analyzed the hydrogen
bond life time correlation function(HBCF) to study the protein water
interactions. At 300K, the result looks good and comparable with the
literature data. But at 250 and 200K, during the initial 0-2ps, HBCF decay
is very fast before it start to relax. This problem does not arise when i
tried with other force field which came along with gromacs package(like
GROMOS,OPLS..) I don't know where i am making mistakes; patching the amber
and charmm force fields to gromacs package lead to this problem?
Can anybody help me? thank you.
My mdp options are:
cpp = /lib/cpp
constraints = hbonds
constraint_algorithm = shake
integrator = md
dt = 0.001 ;
nsteps = 500000 ;
nstcomm = 1 ;
nstlist = 10
ns_type = grid
nstenergy = 5 ;
nstlog = 5 ;
nstvout = 5 ;
nstxout = 5 ;
;nstxtcout = 5 ;
;xtc-precision = 100
nstfout = 0
coulombtype = shift
fourierspacing = 0.12
pme_order = 4
vdwtype = switch
rvdw = 1.0
rlist = 1.2
rcoulomb = 1.0
pbc = xyz
;Berendsen temperature coupling is on
Tcoupl = nose-hoover ; temperature bath (yes, no)
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 200 200
;Berendsen Pressure coupling is on
pcoupl = no ; pressure bath (yes, no)
;Generate velocities is on at 200
gen_vel = no ; generate initial velocities
;gen_temp = 200.0 ; initial temperature
;gen_seed = 173529 ; random seed
;
regards,
Rama
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