[gmx-users] Errors in constraint pulling

[Hideya Nakamura]

Thank you for your suggestions, Berk,

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

I am sure that. I want to set a molecule +3.5 in z from center of the bilayer.

> 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

My box size is approximately 8.0 nm. So, +3.5 is not more than half of
the box in my case.
And also, when I tried +2.1 nm (just above lipid head groups), the
same errors and warnings were observed.

Is there other possible problems?

Hideya




>> 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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