[gmx-users] constraint error

[xiaoyi li]

Dear gmx users,

When I perform a MD run with position restraints, it stopped in a few
steps. In the .log file, it shows:

Constraint error in algorithm Shake at step 0
.
Constraint error in algorithm Shake at step 1
 
Step 1  Warning: pressure scaling more than 1%, mu: 3.0873 3.0873 3.0873
Inner product between old and new vector <= 0.0!
.
Constraint error in algorithm Shake at step 2
 
Step 2  Warning: pressure scaling more than 1%, mu: 1.02276 1.02276
1.02276
Large VCM(group rest):     -0.00235,     -0.00166,      0.00666,
ekin-cm:  1.94487e+00
.

What's the problem? How could I correct it?

Below is my .mdp file:

title               =  Yo
cpp                 =  /lib/cpp
constraints         =  all-bonds
define		    =  -DPOSRES_LIPID
constraint_algorithm=  shake
shake_tol	    =  0.002
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  500000	; total 1000 ps.
nstcomm             =  1
nstxout             =  5000
nstvout             =  5000
nstfout             =  0
nstlog              =  10000
nstenergy           =  500
nstxtcout           =  500
nstlist             =  10
ns_type             =  grid
pbc		    =  xyz
rlist               =  1.0
rcoulomb            =  1.8
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps		    =  IG1	DPPC	SOL
tau_t               =  0.1	0.1	0.1
ref_t               =  300	300	300
; Energy monitoring
energygrps          =  IG1	DPPC	SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          =  isotropic
tau_p               =  1
compressibility     =  4.5e-5
ref_p               =  1
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529



Thanks,

-- 
Xiao-Yi
Department of Cell & Molecular Biology
Uppsala University
Sweden