[gmx-users] Help on umbrella sampling

[Justin A. Lemkul]

raghuvir at bcpindia.org wrote:
> 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}
> 

"Soft core" is a mechanism by which Lennard-Jones interactions are modified 
while doing decoupling/annihilation calculations.  This point is not relevant here.

I see that you're restraining the lipids in some way.  Which atoms are 
restrained?  In which directions?  Why are you restraining them?  I would assume 
that as a molecule is pulled through your membrane, any artificial forces that 
work against one another would cause instability.

-Justin

> Following is the md_pull.mdp file as modified;
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> 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
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Please help me
> 
> Thanks N Regards
> 
> Raghuvir
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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