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
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: xxia...@ust.hk Tel: 23585896
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
