[gmx-users] Errors in constraint pulling

[Berk Hess]

Are you sure your initial distance is -3.5 along (0,0,-1),
this means the distance is actually +3.5 in z.

Another issue could be that 3.5 is more than half the box size.
I think we should add a check for too long distances,
so users get a clear error message and they do not need to contact
the mailing list.

Berk

> Date: Wed, 9 Sep 2009 13:18:04 -0400
> From: hideyanakamura at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Errors in constraint pulling
> 
> Dear GROMACS users,
> 
> I am trying to calculate the potential of mean force (PMF) of a
> molecule (A) across phospholipid bilayer (LIP) using constraint
> method.
> I am using GROMACS ver 4.0.4.
> RUN parameters are as follows
> -------------------------------------------------------------------------------
> integrator               = md
> tinit                    = 0
> dt                       = 0.002 ;[ps]
> nstlist                  = 10 ;[step]
> ns_type                  = grid
> rlist                    = 1.0
> pbc                      = xyz
> 
> coulombtype              = pme
> rcoulomb                 = 1.0	;[nm]
> epsilon-r                = 1    ;(1)
> vdw-type                 = switch
> rvdw-switch              = 0.9 ;[nm]
> rvdw                     = 1.0 ;[nm]
> DispCorr                  = EnerPres
> 
> fourierspacing		 = 0.12 ;[nm] (0.12)
> fourier_nx               = 0       ;(0)
> fourier_ny               = 0       ;(0)
> fourier_nz               = 0       ;(0)
> pme_order                = 4       ;(4)
> ewald_rtol               = 1e-05   ;(1e-5)
> epsilon_surface          = 0       ;(0)
> optimize_fft             = no
> 
> tcoupl			 = berendsen
> tc_grps                  = LIP SOL A
> tau_t                    = 0.1 0.1 0.1 ;[ps]
> ref_t                    = 300 300 300 ;[K]
> Pcoupl                   = berendsen
> Pcoupltype               = semiisotropic   ;useful for membrane	
> tau_p                    = 1.0 1.0         ;[ps]
> compressibility          = 4.5e-05 4.5e-05 ;[bar^-1]
> ref_p                    = 1.0 1.0         ;[bar]
> 
> gen_vel                  = no ;yes or no
> gen_temp                 = 300 ;[K]
> gen_seed                 = 113 ;(173529)
> 
> constraints              = all-bonds  ;all-bonds/none
> constraint-algorithm     = LINCS
> unconstrained-start      = no
> lincs-order              = 4   ;(4)
> lincs-warnangle          = 30  ;(30)
> 
> ; COM PULLING
> pull                     = constraint
> pull_geometry            = direction
> pull_dim                 = N N Y
> pullstart                = no
> pull_nstxout             = 10
> pull_nstfout             = 10
> pull_ngroups             = 1
> pull_group0              = LIP
> pull_group1              = A
> pull_vec1                = 0.0 0.0 -1.0
> pull_init1               = -3.50
> pull_rate1               = 0
> pull_k1                  = 500
> -------------------------------------------------------------------------------
> When I simulated under above parameters, following warnings and errors
> were generated.
> 
> -Warning: pressure scaling more than 1%
> -LINCS warning:
> 
> These errors were always generated when a molecule (pull_gropu1) was
> existing in water phase.
> After simulation, serious disruption of a molecule (pull_gropu1) was observed.
> 
> However, when a molecule (pull_gropu1) was existing inside lipid
> membrane, no error was observed and calculation was successfully
> conducted in constrained simulation.
> 
> I have done long time (5 nsec) simulations before constrained
> simulation using umbrella method, thus I believe the initial condition
> is fully equilibrated.
> 
> Could some one please give me an advice to calculate PMF?
> 
> Sincerely
> 
> 
> ___________________________________________________________________
> Hideya Nakamura, Ph.D.
> 
> Post Doctoral Associate
> University of Florida, Particle Engineering Research Center (PERC)
> mail to: hideyanakamura at gmail.com
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