[gmx-users] Generalized Born segfaults with v4.5.1

[Silvio a Beccara]

Dear friends,

when trying to run a double precision vanilla MD, version 4.5.1, with a small 
hairpin molecule (248 atoms) in implicit solvent (generalized Born 
approximation) this is what I get:

---------------------------------------------------------------------------------------------
Getting Loaded...
Reading file hairpin-md-gb-1.tpr, VERSION 4.5.1 (double precision)
Loaded with Money

starting mdrun 'Protein'
50000 steps,     50.0 ps.
Segmentation fault
---------------------------------------------------------------------------------------------

In some trials, I also get a message about the distance in an 1-4 interaction 
being beyond the table size, but this is not the case.

Strangely enough, the MD runs fine with a development version (4.0.99, 
downloaded from the GIT repository).

I am attaching my mdp and pdb files.


Regards


Silvio a Beccara


Dip. di Fisica - Universita` di Trento
14 Via Sommarive
38123 Povo - TN
tel: 0461-881631
-------------- next part --------------
;
;   Molecular dynamics thermostatted @ 1600.0 K	
;
cpp                 =  /usr/bin/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  md
comm_mode           =  angular
nsteps              =  50000 
dt                  =  0.001
pbc                 =  no
periodic_molecules  =  no
nstcomm             =  10
nstxout             =  10
; nstfout             =  1
ns_type             =  simple
rlist               =  2.0
rcoulomb            =  2.0
rvdw                =  2.0
coulombtype         =  cut-off
vdwtype             =  cut-off
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Nose-Hoover temperature coupling is on in one group
Tcoupl              = nose-hoover
tau_t               = 0.3   
tc-grps             = protein
; Generate velocites is on at 1600.0 K.
gen_vel             = yes
ref_t               = 1600.0
gen_seed            = 312500933 
; no barostat
Pcoupl              = no

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent         = gbsa

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm             = obc
; Frequency of calculating the Born radii inside rlist
nstgbradii               = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                 = 2.0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent       = 78.3
; Salt concentration in M for Generalized Born models
gb_saltconc              = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha             = 1
gb_obc_beta              = 0.8
gb_obc_gamma             = 4.85
gb_dielectric_offset     = 0.009
sa_algorithm             = still
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension       = 2.092
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ratch-frame63.pdb
Type: application/vnd.palm
Size: 37841 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100907/542f22a9/attachment.pdb>