[gmx-users] Implicit solvent crashes with PD

[Justin A. Lemkul]

Hi All,

I'm having a strange problem with some implicit solvent systems and I'm 
wondering if anyone's experienced the same problem or if I've stumbled upon a 
bug.  I'm testing some methodology with a robust system (everyone's favorite, 
1AKI lysozyme).  Running simulations with finite cutoffs works fine (in serial 
or parallel using DD), but if I try to call the all-vs-all kernels (e.g. 
infinite cutoffs), the simulations instantly crash (at step 0) with LINCS 
warnings.  Running in serial, however, produces perfectly stable trajectories 
using all-vs-all, but the simulations are very slow.

The effects are independent of integrator (tested sd and md) and 
hardware/compilers.  The problem is reproducible on two very different systems:

1. x86_64 via OpenMPI 1.4.2 and compiled with cmake with gcc-4.3.4

2. Mac OSX with threads and compiled via autoconf with gcc-4.4.4

All force fields that I've tested (OPLS-AA, CHARMM27, and AMBER03) give the same 
result.

The problem is present in version 4.5.4 and the most current 
release-4-5-patches.  My .mdp file and a gdb backtrace are provided at the end 
of this message.

Is there anything else to try, or should I just file a redmine issue with a .tpr 
file?

-Justin


=== .mdp file ===

constraints         =  all-bonds
integrator          =  sd
dt                  =  0.002    ; ps !
nsteps              =  50000    ; 100 ps
nstlist             =  0
ns_type             =  simple	; grid also fails
rlist               =  0
coulombtype         =  cut-off
vdwtype             =  cut-off
rcoulomb            =  0
rvdw                =  0
pbc                 =  no
epsilon_rf          =  0
rgbradii            =  0
comm_mode           =  angular

implicit_solvent    = GBSA
gb_algorithm        = OBC
gb_epsilon_solvent  = 78.3
sa_surface_tension  = 2.25936

nstxout             = 0
nstfout             = 0
nstvout             = 0
nstxtcout           = 500
nstlog              = 500
nstcalcenergy       = -1
nstenergy           = 500

tc_grps             = system
tau_t               = 1.0
ref_t               = 298

gen_vel             = yes
gen_temp            = 298
gen_seed            = 1023


=== debug output ===

(following the usual LINCS warnings)

(gdb) up
#1  0x002cf045 in pbc_rvec_sub (pbc=0x0, xi=0x62fae58, xj=0xf954c55c, 
dx=0xbfffc1cc) at genborn.c:106
106			rvec_sub(xi,xj,dx);
(gdb) up
#2  0x002d36c0 in gb_bonds_tab (x=0x39000, f=0xdfe000, fshift=0x1033e00, 
charge=0x10d3e00, p_gbtabscale=0x1032028, invsqrta=0x105e000, dvda=0x1060000, 
GBtab=0xb35010, idef=0x1092600, epsilon_r=1, gb_epsilon_solvent=78.3000031, 
facel=137.161057, pbc=0x0, graph=0x0) at genborn.c:1373
1373				ki            = pbc_rvec_sub(pbc,x[ai],x[aj],dx);
(gdb) up
#3  0x002d4829 in calc_gb_forces (cr=0x903890, md=0x905580, born=0x905370, 
top=0x1092600, atype=0x1092b1c, x=0x39000, f=0xdfe000, fr=0x1031e00, 
idef=0x1092600, gb_algorithm=2, sa_algorithm=0, nrnb=0x1031000, bRad=1, 
pbc=0xbfffc5dc, graph=0x0, enerd=0x9070b0) at genborn.c:1680
1680	    enerd->term[F_GBPOL]       += gb_bonds_tab(x,f,fr->fshift, 
md->chargeA,&(fr->gbtabscale),
(gdb) up
#4  0x002a4ee1 in do_force_lowlevel (fplog=0xa07d94c0, step=0, fr=0x1031e00, 
ir=0x1001a00, idef=0x1092600, cr=0x903890, nrnb=0x1031000, wcycle=0x904f30, 
md=0x905580, opts=0x1001c84, x=0x39000, hist=0x907f50, f=0xdfe000, 
enerd=0x9070b0, fcd=0x904e10, mtop=0x900c00, top=0x1092600, born=0x905370, 
atype=0x1092b1c, bBornRadii=1, box=0x907e40, lambda=0, graph=0x0, 
excl=0x1092b44, mu_tot=0x1031e70, flags=501, cycles_pme=0xbfffc914) at force.c:267
267			calc_gb_forces(cr,md,born,top,atype,x,f,fr,idef,
(gdb) up
#5  0x003373d5 in do_force (fplog=0xa07d94c0, cr=0x903890, inputrec=0x1001a00, 
step=0, nrnb=0x1031000, wcycle=0x904f30, top=0x1092600, mtop=0x900c00, 
groups=0x900c70, box=0x907e40, x=0x39000, hist=0x907f50, f=0xdfe000, 
vir_force=0xbfffd4d4, mdatoms=0x905580, enerd=0x9070b0, fcd=0x904e10, lambda=0, 
graph=0x0, fr=0x1031e00, vsite=0x0, mu_tot=0xbfffd434, t=0, field=0x0, ed=0x0, 
bBornRadii=1, flags=501) at sim_util.c:725
725	    do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef),
(gdb) up
#6  0x000173cc in do_md (fplog=0xa07d94c0, cr=0x903890, nfile=28, 
fnm=0xbfffed60, oenv=0x900500, bVerbose=1, bCompact=1, nstglobalcomm=10, 
vsite=0x0, constr=0x905400, stepout=100, ir=0x1001a00, top_global=0x900c00, 
fcd=0x904e10, state_global=0x900d20, mdatoms=0x905580, nrnb=0x1031000, 
wcycle=0x904f30, ed=0x0, fr=0x1031e00, repl_ex_nst=0, repl_ex_seed=-1, 
cpt_period=15, max_hours=-1, deviceOptions=0x24214 "", Flags=7680, 
runtime=0xbfffd758) at md.c:1015
1015	            do_force(fplog,cr,ir,step,nrnb,wcycle,top,top_global,groups,
(gdb) up
#7  0x00013210 in mdrunner (nthreads_requested=2, fplog=0xa07d94c0, cr=0x903890, 
nfile=28, fnm=0xbfffed60, oenv=0x900500, bVerbose=1, bCompact=1, 
nstglobalcomm=-1, ddxyz=0xbfffea10, dd_node_order=1, rdd=0, rconstr=0, 
dddlb_opt=0x2756f "auto", dlb_scale=0.800000012, ddcsx=0x0, ddcsy=0x0, 
ddcsz=0x0, nstepout=100, resetstep=-1, nmultisim=0, repl_ex_nst=0, 
repl_ex_seed=-1, pforce=-1, cpt_period=15, max_hours=-1, deviceOptions=0x24214 
"", Flags=7680) at runner.c:811
811	        integrator[inputrec->eI].func(fplog,cr,nfile,fnm,
(gdb) up
#8  0x0001cb7b in main (argc=7, argv=0xbffff3c8) at mdrun.c:662
662	  rc = mdrunner(nthreads, fplog,cr,NFILE,fnm,oenv,bVerbose,bCompact,


-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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