[gmx-users] Domain decomposition error in alchemical free energy perturbation MD
lina
lina.lastname at gmail.com
Sat Oct 15 13:22:04 CEST 2011
On Sat, Oct 15, 2011 at 2:11 PM, Xiaoxiao He <xxiaohe at ust.hk> wrote:
> Dear all,
> I'm doing an "slow-growth" alchemical free energy perturbation calculation
> of the formation of a disulfide bridge between two Cysteines with Gromacs.
> I've had tried different ways to combine the topology of both state A and
> state B, and finally settled with the most direct way -- to "mutate" the
> atoms that have different partial charges in the two states, and transform
> the two hydrogen atoms into "dummy" atoms. As suggested by Gromacs manual
> and some messages from the internet, I put explicitly the OPLS parameters
> for the bonds, pairs, angles and dihedrals changed from state A to state B,
> and the grompp didn't give a warning. But when I was testing the production
> simulation on two processors, there was a warning of fatal error in the log
> file:
> =========================================================================================
> Initializing Domain Decomposition on 2 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
> two-body bonded interactions: 3.774 nm, LJC Pairs NB, atoms 12 205
> multi-body bonded interactions: 0.640 nm, Ryckaert-Bell., atoms 1013 417
> Minimum cell size due to bonded interactions: 4.151 nm
> Using 0 separate PME nodes
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 2 cells with a minimum initial size of 5.189 nm
> The maximum allowed number of cells is: X 0 Y 0 Z 0
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.4
> Source code file: domdec.c, line: 6436
> Fatal error:
> There is no domain decomposition for 2 nodes that is compatible with the
> given box and a minimum cell size of 5.18876 nm
> Change the number of nodes or mdrun option -rdd or -dds
as suggested by the log:
1] Change the number of nodes
or
2] mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> =============================================================================================
> The atoms indexed 12 and 205 are a CD1 in Leu1 and another CB in Ala12
> respectively. I checked the topology and found no entries containing both
> these atoms. What's weird is that there's no way for these two atoms to have
> bonded interactions, but it says in the log that they have a two-body bonded
> interaction with a distance of 3.774 nm, which I cannot understand.
> Does anyone have an explanation what this could mean? Any suggestion is
> appreciated!
> Thanks in advance!
>
> Xiaoxiao He
> Oct. 15, 2011
>
>
> Attached are the input parameters for the production md:
> =====================================================================
> -Input Parameters:
> integrator = sd
> nsteps = 2000000
> init_step = 0
> ns_type = Grid
> nstlist = 10
> ndelta = 2
> nstcomm = 10
> comm_mode = Linear
> nstlog = 100
> nstxout = 100000
> nstvout = 100000
> nstfout = 100000
> nstcalcenergy = 10
> nstenergy = 100
> nstxtcout = 1000
> init_t = 0
> delta_t = 0.0005
> xtcprec = 1000
> nkx = 36
> nky = 36
> nkz = 36
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = TRUE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = No
> nsttcouple = -1
> epc = Berendsen
> epctype = Isotropic
> nstpcouple = 10
> tau_p = 1
> ref_p (3x3):
> ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> compress (3x3):
> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
> refcoord_scaling = No
> posres_com (3):
> posres_com[0]= 0.00000e+00
> posres_com[1]= 0.00000e+00
> posres_com[2]= 0.00000e+00
> posres_comB (3):
> posres_comB[0]= 0.00000e+00
> posres_comB[1]= 0.00000e+00
> posres_comB[2]= 0.00000e+00
> andersen_seed = 815131
> rlist = 1.3
> rlistlong = 1.3
> rtpi = 0.05
> coulombtype = PME
> rcoulomb_switch = 0
> rcoulomb = 1.3
> vdwtype = Switch
> rvdw_switch = 0.8
> rvdw = 0.9
> epsilon_r = 1
> epsilon_rf = 1
> tabext = 1
> implicit_solvent = No
> gb_algorithm = Still
> gb_epsilon_solvent = 80
> nstgbradii = 1
> rgbradii = 1
> gb_saltconc = 0
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> gb_dielectric_offset = 0.009
> sa_algorithm = Ace-approximation
> sa_surface_tension = 2.05016
> DispCorr = EnerPres
> free_energy = yes
> init_lambda = 0
> delta_lambda = 5e-07
> n_foreign_lambda = 0
> sc_alpha = 0.5
> sc_power = 1
> sc_sigma = 0.3
> sc_sigma_min = 0.3
> nstdhdl = 10
> separate_dhdl_file = no
> dhdl_derivatives = yes
> dh_hist_size = 0
> dh_hist_spacing = 0.1
> nwall = 0
> wall_type = 9-3
> wall_atomtype[0] = -1
> wall_atomtype[1] = -1
> wall_density[0] = 0
> wall_density[1] = 0
> wall_ewald_zfac = 3
> pull = no
> disre = No
> disre_weighting = Conservative
> disre_mixed = FALSE
> dr_fc = 1000
> dr_tau = 0
> nstdisreout = 100
> orires_fc = 0
> orires_tau = 0
> nstorireout = 100
> dihre-fc = 1000
> em_stepsize = 0.01
> em_tol = 10
> niter = 20
> fc_stepsize = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> ConstAlg = Lincs
> shake_tol = 0.0001
> lincs_order = 4
> lincs_warnangle = 30
> lincs_iter = 1
> bd_fric = 0
> ld_seed = 1993
> cos_accel = 0
> deform (3x3):
> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> grpopts:
> nrdf: 3903 22866
> ref_t: 300 300
> tau_t: 0.1 0.1
> anneal: No No
> ann_npoints: 0 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp_flags[ 0]: 0
> efield-x:
> n = 0
> efield-xt:
> n = 0
> efield-y:
> n = 0
> efield-yt:
> n = 0
> efield-z:
> n = 0
> efield-zt:
> n = 0
> bQMMM = FALSE
> QMconstraints = 0
> QMMMscheme = 0
> scalefactor = 1
> qm_opts:
> ngQM = 0
> ======================================================================================================
>
> --
> Xiaoxiao HE
> Department of Chemistry
> The Hong Kong University of Science and Technology
> Clear Water Bay, Kowloon
> Hong Kong
> Email: xxiaohe at ust.hk Tel: 23585896
>
> --
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