[gmx-users] Free energy perturbation - table extension and blowing system

[Krzysztof Makuch]

Ok, I've found what's wrong here. Intramolecular bonded interactions in
large molecule should be changed differently:
couple-intramol          = yes
Maybe somebody will find this useful.

2017-12-18 19:31 GMT+01:00 Krzysztof Makuch <krzysztof.makuch at gmail.com>:

> Hi,
> I want to calculate 'solvation' energy of lutein in bilayer and water by
> Free Energy Perturbation. When I'm running a normal MD, or some kind of
> steering dynamics,my system works just fine. After addition of FEP
> parameters, em runs, but instantly  returns series of warnings:
>
> WARNING: Listed nonbonded interaction between particles 6461 and 6482
> at distance 2.545 which is larger than the table limit 2.200 nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
>
> The same thing repeats for several pairs of atoms, only in one
> transmembrane molecule. As I said, everything is fine without FEP
> parameters. For this instance I'm using the following parameters adapted
> stright from the Bevanlab tutorial:
>
> ; Run control
> integrator               = steep
> nsteps                   = 5000
> ; EM criteria and other stuff
> emtol                    = 100
> emstep                   = 0.01
> niter                    = 20
> nbfgscorr                = 10
> ; Output control
> nstlog                   = 1
> nstenergy                = 1
> ; Neighborsearching and short-range nonbonded interactions
> cutoff-scheme            = verlet
> nstlist                  = 1
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.2
> ; Electrostatics
> coulombtype              = PME
> rcoulomb                 = 1.2
> ; van der Waals
> vdwtype                  = cutoff
> vdw-modifier             = potential-switch
> rvdw-switch              = 1.0
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                  = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
> ; Temperature and pressure coupling are off during EM
> tcoupl                   = no
> pcoupl                   = no
> ; Free energy control stuff
> free_energy              = yes
> init_lambda_state        = 0
> delta_lambda             = 0
> calc_lambda_neighbors    = 1
> ; Vectors of lambda specified here
> ; Each combination is an index that is retrieved from init_lambda_state
> for each simulation
> ; init_lambda_state        0    1    2    3    4    5    6    7    8
> 9    10   11   12   13   14   15   16   17   18   19   20
> vdw_lambdas              = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
> 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
> coul_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> ; We are not transforming any bonded or restrained interactions
> bonded_lambdas           = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> restraint_lambdas        = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> ; Masses are not changing (particle identities are the same at lambda = 0
> and lambda = 1)
> mass_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> ; Not doing simulated temperting here
> temperature_lambdas      = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> ; Options for the decoupling
> sc-alpha                 = 0.5
> sc-coul                  = no
> sc-power                 = 1.0
> sc-sigma                 = 0.3
> couple-moltype           = lutein
> couple-lambda0           = vdw
> couple-lambda1           = none
> couple-intramol          = no
> nstdhdl                  = 10
> ; No velocities during EM
> gen_vel                  = no
> ; options for bonds
> constraints              = h-bonds
> ; Type of constraint algorithm
> constraint-algorithm     = lincs
> ; Do not constrain the starting configuration
> continuation             = no
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order              = 12
>
>
> What I've tried by now and didn't work:
> - I've tried to increase table extension, but it didn't do any good.
> - I've tried to change the charge groups, which are now 1 atom = 1 group
> for this molecule
> - I was trying to solve this with gromacs 4, 5 and 16'. Warnings were
> similar.
> If I try to run further FEP steps the system with FEP parameters blows up.
> MD without FEP simulates doesn't cause any problems.
> My guess is I'm missing something inside FEP parameters. I'm using GROMACS
> for several years by now and for the first time I can't solve the problem
> by myself. I'd be glad for any tips You could give.
> Best,
> Krzysiek
> --
> Jagiellonian University
> Department of Computational Biophysics and Bioinformatics
> tel.1: (12) 664 61 49
> tel.2: (48) 664 086 049
>



-- 
Jagiellonian University
Department of Computational Biophysics and Bioinformatics
tel.1: (12) 664 61 49
tel.2: (48) 664 086 049