[gmx-users] lysine side chain shrinking

[tarak karmakar]

Dear All,


During a simulation of a protein with a ligand, I see the -NH3 of the
lysine side chain near the ligand is getting squeezed for a very short
time; N-H bonds are getting contracted and the angle are no longer within
tetrahedral normal <HNH angles. I have used LINCS to keep all the covalent
C-H, N-H and O-H bonds rigid. I have gone through a string [
http://lists.gromacs.org/pipermail/gmx-users/2010-November/056094.html] in
the mailing list but found little helpful. For my case the simulation does
not give me any warning. Please suggest me if there is any problem with my
simulation protocol.


The '.mdp' file is given as follows

integrator              = md
tinit                   = 0
dt                      = 0.001
nsteps                  = 5000000
nstcomm                 = 1
comm_grps               = system
comm_mode               =linear

; 7.3.8 Output Control
nstxout                 = 5000
nstvout                 = 5000
nstfout                 = 5000
nstlog                  = 2000
nstenergy               = 2000
nstxtcout               = 2000
xtc_precision           = 2000
xtc_grps                = System
energygrps              = System

; 7.3.9 Neighbor Searching
nstlist                 = 10
ns_type                 = grid
pbc                     = xyz
rlist                   = 1.4

; 7.3.10 Electrostatics
coulombtype             = PME
rcoulomb                = 1.4

; 7.3.11 VdW
vdwtype                 = cut-off
rvdw                    = 1.4
DispCorr                = EnerPres

; 7.3.13 Ewald
fourierspacing          = 0.14
pme_order               = 4
ewald_rtol              = 1e-5

; 7.3.14 Temperature Coupling
tcoupl                  = nose-hoover
tc_grps                 = system
tau_t                   = 1.0
ref_t                   = 300

; 7.3.15 Pressure Coupling
pcoupl                  = parrinello-rahman
pcoupltype              = isotropic
tau_p                   = 1.0
compressibility         = 4.5e-5
ref_p                   = 1.0

gen_vel                 = yes
gen_temp                = 300
gen_seed                = 113969

; 7.3.18 Bonds
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
lincs_order             = 4
lincs_iter              = 1
lincs_warnangle         = 30


Thanks,
Tarak