[gmx-users] got seg fault

[gmx at 4ka.mipt.ru]

my mdscript with init values for em and md:
--------------------****---------------
#!/bin/csh

setenv MOL aq
setenv PATH "$PATH\:/usr/home/hello/gromacs/i386_d_g/bin"

echo generating energy minimisation parameter file...
cat > em.mdp << _EOF_

title               =  ${MOL}
cpp                 =  /usr/bin/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
dt                  =  0.001    ; ps !
nsteps              =  1000
nstlist             =  10
ns_type             =  grid
rlist               =  0.7
rcoulomb            =  0.7
rvdw                =  0.7
;
;       Energy minimizing stuff
;
emtol               =  1000.0
emstep              =  0.001
_EOF_
grompp_d -f em -c ${MOL} -p ${MOL} -o ${MOL}_em 
mdrun_d -nice 15 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4md -v  
# main simulation 
# initial values, 
@ T = 300  # T init
@ i = 0    
@ j = 0  
@ Tend = 300     # 
@ delta1 = 1   # delta T during heating, (Tr - T)/delta1    must be int
@ delta2 = -50   # delta T during cooling, (Tr - Tend)/delta2 must be int
@ Tr = 1000        # 
@ fl = 0         # if fl = 1 -- cooling
@ ns1 = 50      # nsteps for heating
@ ns2 = 100     # nsteps for cooling
@ ns3 = 3000    # nsteps for  relax at Tmax
@ ns4 = 10000    # nsteps for  relax at the end
# dumping coords frequency   
@ xout1 = 10	# heating      
@ xout2 = 10	# max T
@ xout3 = 10    # cooling
@ xout4 = 10    # min T
@ xout = $xout1 
@ nsteps = $ns1
@ st = 0
set gen_vel="yes"
#####################
#### main_loop ######
#####################
while 1
### GROMPP MD ###

@ i++

cat > md.mdp << _EOF_
title               =  ${MOL} step $i
cpp                 =  /usr/bin/cpp
constraints         =  none
integrator          =  md
tinit		    =  ${st}e-3	
dt                  =  0.001	; ps !
nsteps              =  $nsteps	; total
nstcomm             =  1
nstxout             =  $xout
nstvout             =  0
nstfout             =  0
nstlist             =  10
ns_type             =  grid
rlist               =  0.7
rcoulomb            =  0.7
rvdw                =  0.7
; Berendsen temperature coupling is on 
Tcoupl              =  berendsen
tau_t               =  0.1
tc-grps		    =  System
ref_t               =  $T	

coulombtype	    = Ewald
fourierspacing	    = 0.6
ewald_rtol	    = 1e-5
pme_order	    = 4

;comm_mode	    = Linear


; Pressure coupling is not on
;Pcoupl              =  Parrinello-Rahman
;tau_p               =  0.5
;compressibility     =  4.5e-5
;ref_p               =  1.0
; Generate velocites is on 


gen_vel              =  $gen_vel
gen_temp             =  300
gen_seed             =  173529

_EOF_

if $j == 0 then
grompp_d -f md -c ${MOL}_b4md  -p ${MOL} -o ${MOL}_md
mdrun_d  -s ${MOL}_md -o ${MOL}_md_after_{$i}_step  -c ${MOL}_after_{$i}_step -v
else 
grompp_d -f md -c ${MOL}_after_{$j}_step  -p ${MOL} -o ${MOL}_md 
mdrun_d  -s ${MOL}_md -o ${MOL}_md_after_{$i}_step  -c ${MOL}_after_{$i}_step -v  

endif

# -s topol.tpr (input)
# -o traj.trr (output)
# -c confout.gro (output)  


@ st = $st + $nsteps  # counts hole namber of steps for tinit

if $fl == 2 then
	break
endif

set gen_vel="yes" 

if $fl == 0 then
	@ nsteps = $ns1
	@ delta  = $delta1
else 
	@ nsteps = $ns2
	@ delta  = $delta2
	@ xout   = $xout3 
endif 

@ j = $i
@ T = $T + $delta

if $T == $Tr then
	@ fl = 1
	@ nsteps = $ns3	          # relax at T max 
	@ xout = $xout2
else if $T == $Tend then          
	@ fl = 2                  
	@ nsteps = $ns4		  # relax at T min
 	@ xout = $xout4	
endif

	
end 
################################
##### end of main_loop #########
################################
### NGMX ###
trjcat -o fixed.trr  ${MOL}_md_after_*   # combine traj. all together
ngmx -f fixed.trr  -s ${MOL}_em  &       # c'est ca 

--------****-----------------------------



my .top:;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;; the parameter level ;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

[ defaults ]
 2 1 ; Buckingam potential  	

[ atomtypes ]
; name      mass   charge	ptype	 	c6	      c12	
 O 	15.99940     -1.200	    A		0.22617E-02   0.74158E-06	 0.0000;
 Si	28.08000      2.400	    A		0.14738E-01   0.22191E-04	 0.0000;


;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;; the molucele level ;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

[ nonbond_params ]
  O       O      2      1.339973E+5          27.6       1.688507E-2
  O      Si      2      1.737112E+6       48.7318       1.288457E-2
  Si 	 Si      2	6.653569E+10      147.586	1.831132E-3
;  Si 	 Si 	 2      0			0       1.831132E-3 
  
[ moleculetype ]
 O	0	; Si

[ atoms ]
 1 	 O	1	O	 O	1	-1.2	 15.99940 

[ moleculetype ]
 SI	0;

[ atoms ]
 1	 Si	1	Si	Si	2	 2.4	 28.08000

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;; the system level ;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

[ system ]
 Silica
  
[ molecules ]
O        162 
Si       81
--------------------***************************
my .gro

 alpha quartz box 3x3x3
243
    1    O    O    1   -0.659    0.913    0.244    0.000   0.000   0.000
    2    O    O    2   -0.659    0.913    0.785    0.000   0.000   0.000
    3    O    O    3   -0.659    0.913    1.325    0.000   0.000   0.000
    4    O    O    4   -0.659    0.789   -0.064    0.000   0.000   0.000
    5    O    O    5   -0.659    0.789    0.476    0.000   0.000   0.000
    6    O    O    6   -0.659    0.789    1.017    0.000   0.000   0.000
    7    O    O    7   -0.461    1.027   -0.425    0.000   0.000   0.000
    8    O    O    8   -0.461    1.027    0.116    0.000   0.000   0.000
<skiped>
  242   Si   Si  242    1.214    0.000    0.901    0.000   0.000   0.000
  243   Si   Si  243    1.214    0.000    1.441    0.000   0.000   0.000
   1.47402   1.27654   1.62156   0.00000   0.00000  -0.73701   0.00000   0.00000   0.00000