[gmx-users] Help on umbrella sampling

[raghuvir at bcpindia.org]

Dear Users and Developers

I am trying to execute md_pull.mdp {given below} on a small molecule  
embedded at the core of lipid bilayer.  I have tried to modify the  
md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling.   
I encounter LINCS warning  (1000) after about 100-110 ps of the  
simulation resulting in termination of mdrun. This occurs when the  
small molecule is near the polar heads.  I understand the system is  
exploding.

I have minimized the system, followed by anneal to 323K then nvt and  
npt after which I perform the md_pull.  How can I soften the core {as  
mentioned in the errors on www.gromacs.org} or any other alternative  
is there adding lincs warning to mdp file {I am not aware}

Following is the md_pull.mdp file as modified;
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title		= Umbrella pulling simulation
define		= -DPOSRES_DPPC
; Run parameters
integrator	= md
dt		= 0.002
tinit		= 0
nsteps		= 100000	; 200 ps
nstcomm		= 1
; Output parameters
nstxout		= 5000		; every 10 ps
nstvout		= 5000
nstfout		= 500
nstxtcout	= 500		; every 1 ps
nstenergy	= 500
; Bond parameters
constraint_algorithm 	= lincs
constraints		= all-bonds
continuation	 	= yes		; continuing from NPT
; Single-range cutoff scheme
nstlist		= 5
ns_type		= grid
rlist		= 1.4
rcoulomb	= 1.4
rvdw		= 1.4
; PME electrostatics parameters
coulombtype	= PME
fourierspacing  = 0.12
fourier_nx	= 0
fourier_ny 	= 0
fourier_nz	= 0
pme_order	= 4
ewald_rtol	= 1e-5
optimize_fft	= yes
; Berendsen temperature coupling is on in two groups
Tcoupl	 	=	Nose-Hoover
tc_grps	=	TPF	DPPC	SOL
tau_t	=	0.1	0.1	0.1
ref_t	=	323	323	323
; Pressure coupling is on
pcoupl		= Parrinello-Rahman	    ; Pressure coupling on in NPT
pcoupltype	= semiisotropic		    ; uniform scaling of x-y box vectors,  
independent z
tau_p		= 2.0			        ; time constant, in ps
ref_p		= 1.0	1.0		        ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5	4.5e-5	; isothermal compressibility, bar^-1
; Generate velocities is off
gen_vel		= no
; Periodic boundary conditions are on in all directions
pbc		= xyz
; Long-range dispersion correction
DispCorr	= EnerPres
; Pull code
pull		= umbrella
pull_geometry	= distance
pull_dim	= N N Y
pull_start	= yes		; define initial COM distance > 0
pull_ngroups	= 1
pull_group0	= DPPC
pull_group1	= TPF
pull_rate1	= 0.01		; 0.01 nm per ps = 10 nm per ns
pull_k1		= 1000		; kJ mol^-1 nm^-2
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Please help me

Thanks N Regards

Raghuvir