[gmx-users] Umbrella Sampling tutorial

[Justin Lemkul]

On 11/30/13 9:22 AM, shahab shariati wrote:
> Dear Justin
>
> My system contains lipid bilayer + drug + water molecules.
>
> I want to calculate Potential of mean force as a function of the
> distance between the centers of mass of drug and the lipid bilayer.
>
> Based on your suggestion I used pull_geometry = position for my case.
>
> After the minimization and equilibration, for Generating Configurations
> step, I used following parameters in the md-pull.mdp file:
> ----------------------------------------------------------------------
> title               = md-pull
> ; Run parameters
> integrator       = md
> nsteps           = 500000
> dt                 = 0.002
> ; Output control
> nstxout          = 1000
> nstvout          = 1000
> nstxtcout       = 1000
> nstenergy       = 1000
> nstlog            = 1000
> energygrps      = CHOL DOPC drg SOL
> ; Bond parameters
> continuation    = yes
> constraint_algorithm = lincs
> constraints      = all-bonds
> lincs_iter         = 1
> lincs_order      = 4
> ; Neighborsearching
> ns_type          = grid
> nstlist            = 5
> rlist                = 1.0
> rcoulomb         = 1.0
> rvdw               = 1.0
> ; Electrostatics
> coulombtype    = PME
> pme_order       = 4
> fourierspacing   = 0.16
> ; Temperature coupling is on
> tcoupl             = V-rescale
> tc-grps            = CHOL_DOPC    drg SOL
> tau_t              = 0.5    0.5       0.5
> ref_t               = 323     323       323
> ; Pressure coupling is on
> pcoupl             = Berendsen
> pcoupltype       = semiisotropic
> tau_p              = 2.0
> ref_p               = 1.0    1.0
> compressibility   = 4.5e-5    4.5e-5
> ; Periodic boundary conditions
> pbc                  = xyz
> ; Dispersion correction
> DispCorr           = EnerPres
> ; Velocity generation
> gen_vel             = no
> ; COM motion removal
> nstcomm           = 1
> comm-mode       = Linear
> comm-grps        = CHOL_DOPC_drg  SOL
> ; Pull code
> pull                  = umbrella
> pull_geometry    = position
> pull_dim            = N N Y
> pull_start          = yes
> pull_ngroups      = 1
> pull_group0        = CHOL_DOPC
> pull_group1        = drg
> pull_rate1          = 0.01
> pull_k1              = 1000
> pull_init1           = 0
> pull_vec1           = 0 0 1
> ---------------------------------------------------------------------------------
>
> Then I used following tools:
>
> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o
> pull.tpr
> mdrun -s pull.tpr
>
> pull.gro file was not created and there are strange pdb files with names:
>
> step240702b_n0.pdb
> step240702c_n0.pdb
> step240704b_n0.pdb
> step240704c_n0.pdb
> step240706b_n0.pdb
> step240706c_n0.pdb
> step240707b_n0.pdb
> step240707c_n0.pdb
> step240708b_n0.pdb
> step240708c_n0.pdb
> step240709b_n0.pdb
> step240709b_n1.pdb
> step240709c_n0.pdb
> step240709c_n1.pdb
>
> While, there should be obtained 500 frames. I saw one of these pdb files by
> VMD,
> (step240708c_n0.pdb). I attached figure related to this pdb in below link:
>
> https://www.dropbox.com/s/6qnn4okv63qieec/pdb%20file.docx
>
> When I use trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep, only 241 gro
> files
> were created from conf0.gro to conf240.gro instead of 501 gro files.
>
> I used same parameters in mdp file except Pull code parameters
> for simulation of my system for 20 ns and there are no problems.
>
> What is the reason of this state? Is my Pull code parameters wrong?
>

Applying the pulling restraint is causing the system to crash halfway through 
the simulation.  There is nothing immediately obvious to me about why it is 
happening.  Check out 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System. 
  Try slower pulling or a weaker force constant.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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