Re: [gmx-users] Grompp Error : Segmentation fault

[Justin A. Lemkul]

Roland Schulz wrote:
Please make sure that the error exists in the latest version. Either 
4.5.1 or if you know how please check the latest GIT version 
from release-4-5-patches. If you still get the error with the latest 
version, please file a bugzilla report and attach all required files.




My first guess would be that these lines are problematic:

; Include TFO topology
#include TFO_amber99.itp

The .itp filename should be enclosed in quotes.

-Justin

On Tue, Sep 28, 2010 at 9:01 AM, Alep Latep > wrote:


Dear Gromacs Users and Developers,

I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my
ionic liquid MD simulation using amber 99 force field. I got my
topology from topolbuild v 1.3. I successfully minimized both cation
and anion separately using cg and steep. Then I include the anion in
the cation system using genbox. I got error from grompp like this: 
--

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
processing topology...
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Segmentation fault (core dumped)
[a...@neox MD1]$ 
-

Still cant find my answer in the mailing list. Sorry for the large
post, but here's my .mdp and .top


-
title = Conjugated-Gradients Energy Minimization

; Preprocessing
cpp = /lib/cpp
include = -I../top

; Parameters
integrator = cg
emtol = 1.0
nsteps = 5000
nstenergy = 100
nstxtcout = 100
xtc_grps = System
energygrps = System

; Neighboursearching
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
constraints = none
pbc = xyz

-
; Topology from .mol2 file
; topolbuild version 1.3
; Command line:
; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME
;
; The force field files to be included
#include "amber99.ff/forcefield.itp"

 [ moleculetype ]
; name  nrexcl
BMIM   3

 [ atoms ]
;  nrtype   resnr   residu   atom   cgnrcharge  mass
1  CT 1  BMIM   C1  -0.17243  12.01100  
;  -0.1724300
2  HC 1  BMIM   H1   0.07139   1.00800  
;  -0.1010400
3  HC 1  BMIM   H1   0.05434   1.00800  
;  -0.0467000
4  HC 1  BMIM   H1   0.05138   1.00800  
;   0.0046800
5  CT 1  BMIM   C2   0.02353  12.01100  
;   0.0282100
6  HC 1  BMIM   H2   0.02417   1.00800  
;   0.0523800
7  HC 1  BMIM   H2   0.02427   1.00800  
;   0.0766500
8  CT 1  BMIM   C3   0.01014  12.01100  
;   0.0867900
9  HC 1  BMIM   H3   0.03312   1.00800  
;   0.1199100
   10  HC 1  BMIM   H3   0.02952   1.00800  
;   0.1494300
   11  NA 1  BMIM   N4   0.05435  14.00670  
;   0.2037800
   12  CC 1  BMIM   C4  -0.17380  12.01100  
;   0.0299800
   13  H4 1  BMIM   H4   0.23709   1.00800  
;   0.2670700
   14  NA 1  BMIM   N6   0.07275  14.00670  
;   0.3398200
   15  CT 1  BMIM   C5  -0.07367  12.01100  
;   0.2661500
   16  H1 1  BMIM   H5   0.10657   1.00800  
;   0.3727200
   17  H1 1  BMIM   H5   0.09108   1.00800  
;   0.4638000
   18  CC 1  BMIM   C6  -0.08433  12.01100  
;   0.3794700
   19  H4 1  BMIM   H6   0.20500   1.00800  
;   0.5844700
   20  CR 1  BMIM   C7  -0.02624  12.01100  
;   0.5582300
   21  H5 1  BMIM   H7   0.21862   1.00800  
;   0.7768500
   22  CT 1  BMIM   C8  -0.18403  12.01100  
;   0.5928200
   23  H1 1  BMIM   H8   0.13823   1.00800  
;   0.7310500
   24  H1 1  BMIM   H8   0.13886   1.00800  
;   0.8699100
   25  H1 1  BMIM   H8   0.13010   1.00800  
;   1.100

; total molecu

Re: [gmx-users] Grompp Error : Segmentation fault

[Roland Schulz]

Please make sure that the error exists in the latest version. Either 4.5.1
or if you know how please check the latest GIT version
from release-4-5-patches. If you still get the error with the latest
version, please file a bugzilla report and attach all required files.

On Tue, Sep 28, 2010 at 9:01 AM, Alep Latep wrote:

> Dear Gromacs Users and Developers,
>
> I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic
> liquid MD simulation using amber 99 force field. I got my topology from
> topolbuild v 1.3. I successfully minimized both cation and anion separately
> using cg and steep. Then I include the anion in the cation system using
> genbox. I got error from grompp like this:
>
> --
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> checking input for internal consistency...
> processing topology...
> Generated 2211 of the 2211 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2211 of the 2211 1-4 parameter combinations
> Segmentation fault (core dumped)
> [a...@neox MD1]$
>
> -
> Still cant find my answer in the mailing list. Sorry for the large post,
> but here's my .mdp and .top
>
>
> -
> title = Conjugated-Gradients Energy Minimization
>
> ; Preprocessing
> cpp = /lib/cpp
> include = -I../top
>
> ; Parameters
> integrator = cg
> emtol = 1.0
> nsteps = 5000
> nstenergy = 100
> nstxtcout = 100
> xtc_grps = System
> energygrps = System
>
> ; Neighboursearching
> nstlist = 5
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 0.9
> constraints = none
> pbc = xyz
>
> -
> ; Topology from .mol2 file
> ; topolbuild version 1.3
> ; Command line:
> ; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME
> ;
> ; The force field files to be included
> #include "amber99.ff/forcefield.itp"
>
>  [ moleculetype ]
> ; name  nrexcl
> BMIM   3
>
>  [ atoms ]
> ;  nrtype   resnr   residu   atom   cgnrcharge  mass
> 1  CT 1  BMIM   C1  -0.17243  12.01100   ;
>  -0.1724300
> 2  HC 1  BMIM   H1   0.07139   1.00800   ;
>  -0.1010400
> 3  HC 1  BMIM   H1   0.05434   1.00800   ;
>  -0.0467000
> 4  HC 1  BMIM   H1   0.05138   1.00800   ;
>   0.0046800
> 5  CT 1  BMIM   C2   0.02353  12.01100   ;
>   0.0282100
> 6  HC 1  BMIM   H2   0.02417   1.00800   ;
>   0.0523800
> 7  HC 1  BMIM   H2   0.02427   1.00800   ;
>   0.0766500
> 8  CT 1  BMIM   C3   0.01014  12.01100   ;
>   0.0867900
> 9  HC 1  BMIM   H3   0.03312   1.00800   ;
>   0.1199100
>10  HC 1  BMIM   H3   0.02952   1.00800   ;
>   0.1494300
>11  NA 1  BMIM   N4   0.05435  14.00670   ;
>   0.2037800
>12  CC 1  BMIM   C4  -0.17380  12.01100   ;
>   0.0299800
>13  H4 1  BMIM   H4   0.23709   1.00800   ;
>   0.2670700
>14  NA 1  BMIM   N6   0.07275  14.00670   ;
>   0.3398200
>15  CT 1  BMIM   C5  -0.07367  12.01100   ;
>   0.2661500
>16  H1 1  BMIM   H5   0.10657   1.00800   ;
>   0.3727200
>17  H1 1  BMIM   H5   0.09108   1.00800   ;
>   0.4638000
>18  CC 1  BMIM   C6  -0.08433  12.01100   ;
>   0.3794700
>19  H4 1  BMIM   H6   0.20500   1.00800   ;
>   0.5844700
>20  CR 1  BMIM   C7  -0.02624  12.01100   ;
>   0.5582300
>21  H5 1  BMIM   H7   0.21862   1.00800   ;
>   0.7768500
>22  CT 1  BMIM   C8  -0.18403  12.01100   ;
>   0.5928200
>23  H1 1  BMIM   H8   0.13823   1.00800   ;
>   0.7310500
>24  H1 1  BMIM   H8   0.13886   1.00800   ;
>   0.8699100
>25  H1 1  BMIM   H8   0.13010   1.00800   ;
>   1.100
> ; total molecule charge =   1.100
>
>  [ bonds ]
> ;   ai  aj   funct  b0  kb
>1 5   1 0.15260  259408.   ; C- C
>1 2   1 0.10900  284512.   ; C- H
>1 3   1 0.10900  284512.   ; C- H
>1 4   1 0.10900  284512.   ; C- H
>5 8   1 0.15260  259408.   ; C- C
>5 6 

Re: [gmx-users] Grompp Error : Segmentation fault

[Florian Dommert]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello,

 I am really curious that amber has support for Room Temperature Ionic
liquids ? Can you please provide me a reference how this force field
works for this kind of liquids.

/Flo



On 09/28/2010 03:01 PM, Alep Latep wrote:
> Dear Gromacs Users and Developers,
> 
> I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my
> ionic liquid MD simulation using amber 99 force field. I got my topology
> from topolbuild v 1.3. I successfully minimized both cation and anion
> separately using cg and steep. Then I include the anion in the cation
> system using genbox. I got error from grompp like this: 
> --
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> checking input for internal consistency...
> processing topology...
> Generated 2211 of the 2211 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2211 of the 2211 1-4 parameter combinations
> Segmentation fault (core dumped)
> [a...@neox MD1]$ 
> -
> Still cant find my answer in the mailing list. Sorry for the large post,
> but here's my .mdp and .top
> 
> -
> title = Conjugated-Gradients Energy Minimization
> 
> ; Preprocessing
> cpp = /lib/cpp
> include = -I../top
> 
> ; Parameters
> integrator = cg
> emtol = 1.0
> nsteps = 5000
> nstenergy = 100
> nstxtcout = 100
> xtc_grps = System
> energygrps = System
> 
> ; Neighboursearching
> nstlist = 5
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 0.9
> constraints = none
> pbc = xyz
> -
> ; Topology from .mol2 file
> ; topolbuild version 1.3
> ; Command line:
> ; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME
> ;
> ; The force field files to be included
> #include "amber99.ff/forcefield.itp"
> 
>  [ moleculetype ]
> ; name  nrexcl
> BMIM   3
> 
>  [ atoms ]
> ;  nrtype   resnr   residu   atom   cgnrcharge  mass
> 1  CT 1  BMIM   C1  -0.17243  12.01100  
> ;  -0.1724300
> 2  HC 1  BMIM   H1   0.07139   1.00800  
> ;  -0.1010400
> 3  HC 1  BMIM   H1   0.05434   1.00800  
> ;  -0.0467000
> 4  HC 1  BMIM   H1   0.05138   1.00800  
> ;   0.0046800
> 5  CT 1  BMIM   C2   0.02353  12.01100  
> ;   0.0282100
> 6  HC 1  BMIM   H2   0.02417   1.00800  
> ;   0.0523800
> 7  HC 1  BMIM   H2   0.02427   1.00800  
> ;   0.0766500
> 8  CT 1  BMIM   C3   0.01014  12.01100  
> ;   0.0867900
> 9  HC 1  BMIM   H3   0.03312   1.00800  
> ;   0.1199100
>10  HC 1  BMIM   H3   0.02952   1.00800  
> ;   0.1494300
>11  NA 1  BMIM   N4   0.05435  14.00670  
> ;   0.2037800
>12  CC 1  BMIM   C4  -0.17380  12.01100  
> ;   0.0299800
>13  H4 1  BMIM   H4   0.23709   1.00800  
> ;   0.2670700
>14  NA 1  BMIM   N6   0.07275  14.00670  
> ;   0.3398200
>15  CT 1  BMIM   C5  -0.07367  12.01100  
> ;   0.2661500
>16  H1 1  BMIM   H5   0.10657   1.00800  
> ;   0.3727200
>17  H1 1  BMIM   H5   0.09108   1.00800  
> ;   0.4638000
>18  CC 1  BMIM   C6  -0.08433  12.01100  
> ;   0.3794700
>19  H4 1  BMIM   H6   0.20500   1.00800  
> ;   0.5844700
>20  CR 1  BMIM   C7  -0.02624  12.01100  
> ;   0.5582300
>21  H5 1  BMIM   H7   0.21862   1.00800  
> ;   0.7768500
>22  CT 1  BMIM   C8  -0.18403  12.01100  
> ;   0.5928200
>23  H1 1  BMIM   H8   0.13823   1.00800  
> ;   0.7310500
>24  H1 1  BMIM   H8   0.13886   1.00800  
> ;   0.8699100
>25  H1 1  BMIM   H8   0.13010   1.00800  
> ;   1.100
> ; total molecule charge =   1.100
> 
>  [ bonds ]
> ;   ai  aj   funct  b0  kb
>1 5   1 0.15260  259408.   ; C- C
>1 2   1 0.10900  284512.   ; C- H
>1 3   1 0.10900  284512.   ; C- H
>1 4   1 0.10900  284512.   ; C- H
>5 8   1 0.15260  259408.   ; C- C
>5 6   1 0.10900  284511.   ; C

[gmx-users] Grompp Error : Segmentation fault

[Alep Latep]

Dear Gromacs Users and Developers,

I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic
liquid MD simulation using amber 99 force field. I got my topology from
topolbuild v 1.3. I successfully minimized both cation and anion separately
using cg and steep. Then I include the anion in the cation system using
genbox. I got error from grompp like this:
--
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
processing topology...
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Segmentation fault (core dumped)
[a...@neox MD1]$
-
Still cant find my answer in the mailing list. Sorry for the large post, but
here's my .mdp and .top

-
title = Conjugated-Gradients Energy Minimization

; Preprocessing
cpp = /lib/cpp
include = -I../top

; Parameters
integrator = cg
emtol = 1.0
nsteps = 5000
nstenergy = 100
nstxtcout = 100
xtc_grps = System
energygrps = System

; Neighboursearching
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
constraints = none
pbc = xyz
-
; Topology from .mol2 file
; topolbuild version 1.3
; Command line:
; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME
;
; The force field files to be included
#include "amber99.ff/forcefield.itp"

 [ moleculetype ]
; name  nrexcl
BMIM   3

 [ atoms ]
;  nrtype   resnr   residu   atom   cgnrcharge  mass
1  CT 1  BMIM   C1  -0.17243  12.01100   ;
 -0.1724300
2  HC 1  BMIM   H1   0.07139   1.00800   ;
 -0.1010400
3  HC 1  BMIM   H1   0.05434   1.00800   ;
 -0.0467000
4  HC 1  BMIM   H1   0.05138   1.00800   ;
0.0046800
5  CT 1  BMIM   C2   0.02353  12.01100   ;
0.0282100
6  HC 1  BMIM   H2   0.02417   1.00800   ;
0.0523800
7  HC 1  BMIM   H2   0.02427   1.00800   ;
0.0766500
8  CT 1  BMIM   C3   0.01014  12.01100   ;
0.0867900
9  HC 1  BMIM   H3   0.03312   1.00800   ;
0.1199100
   10  HC 1  BMIM   H3   0.02952   1.00800   ;
0.1494300
   11  NA 1  BMIM   N4   0.05435  14.00670   ;
0.2037800
   12  CC 1  BMIM   C4  -0.17380  12.01100   ;
0.0299800
   13  H4 1  BMIM   H4   0.23709   1.00800   ;
0.2670700
   14  NA 1  BMIM   N6   0.07275  14.00670   ;
0.3398200
   15  CT 1  BMIM   C5  -0.07367  12.01100   ;
0.2661500
   16  H1 1  BMIM   H5   0.10657   1.00800   ;
0.3727200
   17  H1 1  BMIM   H5   0.09108   1.00800   ;
0.4638000
   18  CC 1  BMIM   C6  -0.08433  12.01100   ;
0.3794700
   19  H4 1  BMIM   H6   0.20500   1.00800   ;
0.5844700
   20  CR 1  BMIM   C7  -0.02624  12.01100   ;
0.5582300
   21  H5 1  BMIM   H7   0.21862   1.00800   ;
0.7768500
   22  CT 1  BMIM   C8  -0.18403  12.01100   ;
0.5928200
   23  H1 1  BMIM   H8   0.13823   1.00800   ;
0.7310500
   24  H1 1  BMIM   H8   0.13886   1.00800   ;
0.8699100
   25  H1 1  BMIM   H8   0.13010   1.00800   ;
1.100
; total molecule charge =   1.100

 [ bonds ]
;   ai  aj   funct  b0  kb
   1 5   1 0.15260  259408.   ; C- C
   1 2   1 0.10900  284512.   ; C- H
   1 3   1 0.10900  284512.   ; C- H
   1 4   1 0.10900  284512.   ; C- H
   5 8   1 0.15260  259408.   ; C- C
   5 6   1 0.10900  284511.   ; C- H
   5 7   1 0.10900  284512.   ; C- H
   815   1 0.15260  259408.   ; C- C
   8 9   1 0.10900  284512.   ; C- H
   810   1 0.10900  284512.   ; C- H
  1112   1 0.13850  353129.   ; N- C
  1115   1 0.13850  353129.   ; N- C
  1120   1 0.13850  353129.   ; N- C
  1218   1 0.14000  392459.   ; C- C
  1213   1 0.10800  

Re: [gmx-users] grompp error(Segmentation fault)

[Justin A. Lemkul]

Arik Cohen wrote:
In continuation with my previous e-mail, I'm sorry to continue bothering 
you with this but after reevaluating, it seems that problem might just 
be with the amber forcefield after all as I  manged to run grompp just 
fine and to start the minimization by applying the OPLS forcefield(with 
another OPLS compatible protein: bpti).
I'm still interested in running my program with the amber forcefiled as 
to be compatible with other calculations being done in the group.

I would be most thankful for any suggestion you might have.



You get the seg fault right after ffamber99sbbon.itp is opened.  Are there bad 
lines in it?  In the latest ffamber ports (for version 4.0), there are two files 
- "ffamber99sbbon.itp" and "ffamber99sbbon.itp.bad."  Perhaps there has been 
some pertinent change since you've obtained the ffamber ports.  Do other AMBER 
force fields work for your system of interest, like ffamber99 or ffamber03?  If 
so, it would suggest that the integrity of one or more ffamber99sb* files has 
been somehow compromised.


-Justin


Thanks a lot

Arik

On 4/24/2010 5:23 PM, Arik Cohen wrote:

Thanks again for the ultrafast response.

1. The extra '.' is a typo. (I apologize for that). In the command the 
file name appears as 1bgq_Complex_b4ion.tpr
in addition, Both the single precision and double 
precision(grompp_d) gives this error.
The compilation was done with gcc-4.4.3 with and without the 
option of --disable-float for the double and single precision 
version   respectively.


2a. This is the first call to grompp

b. The following programs such as pdb2gmx_d, editconf_d and genbox are 
working properly.


c.grompp/_d -h  is working , giving a description on the program with 
the different options available.


3. With regards of running grompp with different forcefield
 
*Apparently the problem is with the l-bfgs option in the em.mdp file. 
This is due to the fact that when changing the integrator option to 
steep, the program runs fine   *


I'm sorry but I just saw this now.

The  l-bfgs integrator was chosen since I need to do normal mode analysis

Thanks a lot

Arik


On 4/24/2010 2:26 PM, Justin A. Lemkul wrote:

I suppose the next set of questions to ask would be:

1. How was Gromacs compiled?  What options were specified?
2. Does every instance of grompp fail?  Do other inputs work?  What 
does "grompp -h" do?
3. Does grompp seg fault with totally different systems (different 
force fields)?


-Justin

Arik Cohen wrote:
Thank a lot for your very fast response !. Here are the requested 
details:


1. Version 4.07 is being used.

2. Upgrading from version 4.04 to 4.07 doesn't help.

3. The grompp command given is:

grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 
1bgq_Complex.top -o 1bgq_Complex_b4ion..tpr


4. em.mdp:

integrator  =  l-bfgs
nsteps  =  5
nstlist =  1
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdw-type=  cut-off
rvdw=  1.0
nstenergy   =  10
emtol=  5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0
define  =  -DFLEXIBLE ; using flexible water model


5. The grompp command is issued in this case, before genion. 
However, even when running it alone the same problem arises.


6. The program is being run on Fedora 12 inside 
VMware(2.6.32.11-99.fc12.i686, 32-bit).


7. Running the same command on another OS and type of 
machine(fc10.x86_64) does not solve the problem


7. The output:

  :-)  G  R  O  M  A  C  S  (-:

 Gnomes, ROck Monsters And Chili Sauce

:-)  VERSION 4.0.7  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and 
others.
   Copyright (c) 1991-2000, University of Groningen, The 
Netherlands.

 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

 :-)  grompp_d (double precision)  (-:

Option Filename  Type Description

  -f MDP/em.mdp  Input, Opt!  grompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c 1bgq_Complex_b4ion.pdb  InputStructure file: gro g96 
pdb tpr tpb

   tpa
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr 
tpb tpa
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr 
tpb tpa

  -n  index.ndx  Input, Opt.  Index file
  -p 1bgq_Complex.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology 

Re: [gmx-users] grompp error(Segmentation fault)

[Arik Cohen]

In continuation with my previous e-mail, I'm sorry to continue bothering 
you with this but after reevaluating, it seems that problem might just 
be with the amber forcefield after all as I  manged to run grompp just 
fine and to start the minimization by applying the OPLS forcefield(with 
another OPLS compatible protein: bpti).
I'm still interested in running my program with the amber forcefiled as 
to be compatible with other calculations being done in the group.

I would be most thankful for any suggestion you might have.

Thanks a lot

Arik

On 4/24/2010 5:23 PM, Arik Cohen wrote:

Thanks again for the ultrafast response.

1. The extra '.' is a typo. (I apologize for that). In the command the 
file name appears as 1bgq_Complex_b4ion.tpr
in addition, Both the single precision and double 
precision(grompp_d) gives this error.
The compilation was done with gcc-4.4.3 with and without the 
option of --disable-float for the double and single precision 
version   respectively.


2a. This is the first call to grompp

b. The following programs such as pdb2gmx_d, editconf_d and genbox are 
working properly.


c.grompp/_d -h  is working , giving a description on the program with 
the different options available.


3. With regards of running grompp with different forcefield

*Apparently the problem is with the l-bfgs option in the em.mdp file. 
This is due to the fact that when changing the integrator option to 
steep, the program runs fine *


I'm sorry but I just saw this now.

The  l-bfgs integrator was chosen since I need to do normal mode analysis

Thanks a lot

Arik


On 4/24/2010 2:26 PM, Justin A. Lemkul wrote:

I suppose the next set of questions to ask would be:

1. How was Gromacs compiled?  What options were specified?
2. Does every instance of grompp fail?  Do other inputs work?  What 
does "grompp -h" do?
3. Does grompp seg fault with totally different systems (different 
force fields)?


-Justin

Arik Cohen wrote:
Thank a lot for your very fast response !. Here are the requested 
details:


1. Version 4.07 is being used.

2. Upgrading from version 4.04 to 4.07 doesn't help.

3. The grompp command given is:

grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 
1bgq_Complex.top -o 1bgq_Complex_b4ion..tpr


4. em.mdp:

integrator  =  l-bfgs
nsteps  =  5
nstlist =  1
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdw-type=  cut-off
rvdw=  1.0
nstenergy   =  10
emtol=  5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0
define  =  -DFLEXIBLE ; using flexible water model


5. The grompp command is issued in this case, before genion. 
However, even when running it alone the same problem arises.


6. The program is being run on Fedora 12 inside 
VMware(2.6.32.11-99.fc12.i686, 32-bit).


7. Running the same command on another OS and type of 
machine(fc10.x86_64) does not solve the problem


7. The output:

  :-)  G  R  O  M  A  C  S  (-:

 Gnomes, ROck Monsters And Chili Sauce

:-)  VERSION 4.0.7  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and 
others.
   Copyright (c) 1991-2000, University of Groningen, The 
Netherlands.

 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

 :-)  grompp_d (double precision)  (-:

Option Filename  Type Description

  -f MDP/em.mdp  Input, Opt!  grompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c 1bgq_Complex_b4ion.pdb  InputStructure file: gro g96 
pdb tpr tpb

   tpa
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr 
tpb tpa
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr 
tpb tpa

  -n  index.ndx  Input, Opt.  Index file
  -p 1bgq_Complex.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o 1bgq_Complex_b4ion..tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj 
cpt

  -e   ener.edr  Input, Opt.  Energy file: edr ene

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-[no]v   bool   yes Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes R

Re: [gmx-users] grompp error(Segmentation fault)

[Arik Cohen]

Thanks again for the ultrafast response.

1. The extra '.' is a typo. (I apologize for that). In the command the 
file name appears as 1bgq_Complex_b4ion.tpr
in addition, Both the single precision and double 
precision(grompp_d) gives this error.
The compilation was done with gcc-4.4.3 with and without the option 
of --disable-float for the double and single precision version   
respectively.


2a. This is the first call to grompp

b. The following programs such as pdb2gmx_d, editconf_d and genbox are 
working properly.


c.grompp/_d -h  is working , giving a description on the program with 
the different options available.


3. With regards of running grompp with different forcefield

*Apparently the problem is with the l-bfgs option in the em.mdp file. 
This is due to the fact that when changing the integrator option to 
steep, the program runs fine *


I'm sorry but I just saw this now.

The  l-bfgs integrator was chosen since I need to do normal mode analysis

Thanks a lot

Arik


On 4/24/2010 2:26 PM, Justin A. Lemkul wrote:

I suppose the next set of questions to ask would be:

1. How was Gromacs compiled?  What options were specified?
2. Does every instance of grompp fail?  Do other inputs work?  What 
does "grompp -h" do?
3. Does grompp seg fault with totally different systems (different 
force fields)?


-Justin

Arik Cohen wrote:
Thank a lot for your very fast response !. Here are the requested 
details:


1. Version 4.07 is being used.

2. Upgrading from version 4.04 to 4.07 doesn't help.

3. The grompp command given is:

grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 
1bgq_Complex.top -o 1bgq_Complex_b4ion..tpr


4. em.mdp:

integrator  =  l-bfgs
nsteps  =  5
nstlist =  1
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdw-type=  cut-off
rvdw=  1.0
nstenergy   =  10
emtol=  5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0
define  =  -DFLEXIBLE ; using flexible water model


5. The grompp command is issued in this case, before genion. However, 
even when running it alone the same problem arises.


6. The program is being run on Fedora 12 inside 
VMware(2.6.32.11-99.fc12.i686, 32-bit).


7. Running the same command on another OS and type of 
machine(fc10.x86_64) does not solve the problem


7. The output:

  :-)  G  R  O  M  A  C  S  (-:

 Gnomes, ROck Monsters And Chili Sauce

:-)  VERSION 4.0.7  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and 
others.
   Copyright (c) 1991-2000, University of Groningen, The 
Netherlands.

 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

 :-)  grompp_d (double precision)  (-:

Option Filename  Type Description

  -f MDP/em.mdp  Input, Opt!  grompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c 1bgq_Complex_b4ion.pdb  InputStructure file: gro g96 pdb 
tpr tpb

   tpa
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb 
tpa
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb 
tpa

  -n  index.ndx  Input, Opt.  Index file
  -p 1bgq_Complex.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o 1bgq_Complex_b4ion..tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file: edr ene

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-[no]v   bool   yes Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with 
virtual

sites
-maxwarn int0   Number of allowed warnings during input 
processing
-[no]zerobool   no  Set parameters for bonded interactions 
without
defaults to zero instead of generating an 
error

-[no]renum   bool   yes Renumber atomtypes and minimize number of
atomtypes

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...

WARNING 1 [file MDP/em.mdp, li

Re: [gmx-users] grompp error(Segmentation fault)

[Mark Abraham]

On 25/04/2010 6:28 AM, Arik Cohen wrote:

Thank a lot for your very fast response !. Here are the requested details:

1. Version 4.07 is being used.

2. Upgrading from version 4.04 to 4.07 doesn't help.

3. The grompp command given is:

grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top -o
1bgq_Complex_b4ion..tpr


Last time you gave this command line, your final filename had only one 
period in it. Now it has two. This can be one reason why people giving 
help want to see copy-pasted inputs and outputs, not things filtered 
through people's heads :-)


Since the segfault is arising during the handling of files early in 
grompp, perhaps this double period is the cause of the problem (even 
though it should not be a problem in principle!). Try a normal filename 
with one period.


Mark


4. em.mdp:

integrator = l-bfgs
nsteps = 5
nstlist = 1
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
nstenergy = 10
emtol = 5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0
define = -DFLEXIBLE ; using flexible water model


5. The grompp command is issued in this case, before genion. However,
even when running it alone the same problem arises.

6. The program is being run on Fedora 12 inside
VMware(2.6.32.11-99.fc12.i686, 32-bit).

7. Running the same command on another OS and type of
machine(fc10.x86_64) does not solve the problem

7. The output:

:-) G R O M A C S (-:

Gnomes, ROck Monsters And Chili Sauce

:-) VERSION 4.0.7 (-:


Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

:-) grompp_d (double precision) (-:

Option Filename Type Description

-f MDP/em.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c 1bgq_Complex_b4ion.pdb Input Structure file: gro g96 pdb tpr tpb
tpa
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p 1bgq_Complex.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o 1bgq_Complex_b4ion..tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file: edr ene

Option Type Value Description
--
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input processing
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...

WARNING 1 [file MDP/em.mdp, line unknown]:
For efficient BFGS minimization, use switch/shift/pme instead of cut-off.

processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top//ffamber99sb.itp
Opening library file
/usr/local/gromacs/share/gromacs/top//ffamber99sbnb.itp
Opening library file
/usr/local/gromacs/share/gromacs/top//ffamber99sbbon.itp
Segmentation fault (core dumped)


Thanks a lot in advance for all your help

Arik


On 4/23/2010 4:45 PM, Mark Abraham wrote:

On 24/04/2010 7:28 AM, Arik Cohen wrote:

I'll be most thankful if any one would be able to help me with the
following problem.


Giving more complete information will give you a much better chance.
It's not our job to be the family doctor and ask questions :-)

What GROMACS version is it? Does upgrading to 4.0.7 help?


While running the grompp (in both single and double precision) command I
get a Segmentation fault (core dumped) error.


When? What was the output to date?


The error persist even
after recompiling the GROMACS with gcc-4.4.3(previously I was running
4.04 compiled with the buggy gcc-4.1 compiler).


Does it happen on another machine?


The command I'm using is:

grompp_d -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top -o
1bgq.tpr


What's in the .mdp file?

Mark

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it 

Re: [gmx-users] grompp error(Segmentation fault)

[Justin A. Lemkul]

I suppose the next set of questions to ask would be:

1. How was Gromacs compiled?  What options were specified?
2. Does every instance of grompp fail?  Do other inputs work?  What does "grompp 
-h" do?

3. Does grompp seg fault with totally different systems (different force 
fields)?

-Justin

Arik Cohen wrote:

Thank a lot for your very fast response !. Here are the requested details:

1. Version 4.07 is being used.

2. Upgrading from version 4.04 to 4.07 doesn't help.

3. The grompp command given is:

grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top 
-o 1bgq_Complex_b4ion..tpr


4. em.mdp:

integrator  =  l-bfgs
nsteps  =  5
nstlist =  1
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdw-type=  cut-off
rvdw=  1.0
nstenergy   =  10
emtol=  5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0
define  =  -DFLEXIBLE ; using flexible water model


5. The grompp command is issued in this case, before genion. However, 
even when running it alone the same problem arises.


6. The program is being run on Fedora 12 inside 
VMware(2.6.32.11-99.fc12.i686, 32-bit).


7. Running the same command on another OS and type of 
machine(fc10.x86_64) does not solve the problem


7. The output:

  :-)  G  R  O  M  A  C  S  (-:

 Gnomes, ROck Monsters And Chili Sauce

:-)  VERSION 4.0.7  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

 :-)  grompp_d (double precision)  (-:

Option Filename  Type Description

  -f MDP/em.mdp  Input, Opt!  grompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c 1bgq_Complex_b4ion.pdb  InputStructure file: gro g96 pdb 
tpr tpb

   tpa
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n  index.ndx  Input, Opt.  Index file
  -p 1bgq_Complex.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o 1bgq_Complex_b4ion..tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file: edr ene

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-[no]v   bool   yes Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with 
virtual

sites
-maxwarn int0   Number of allowed warnings during input 
processing

-[no]zerobool   no  Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum   bool   yes Renumber atomtypes and minimize number of
atomtypes

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...

WARNING 1 [file MDP/em.mdp, line unknown]:
  For efficient BFGS minimization, use switch/shift/pme instead of cut-off.

processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top//ffamber99sb.itp
Opening library file 
/usr/local/gromacs/share/gromacs/top//ffamber99sbnb.itp
Opening library file 
/usr/local/gromacs/share/gromacs/top//ffamber99sbbon.itp

Segmentation fault (core dumped)


Thanks a lot in advance for all your help

Arik


On 4/23/2010 4:45 PM, Mark Abraham wrote:

On 24/04/2010 7:28 AM, Arik Cohen wrote:

I'll be most thankful if any one would be able to help me with the
following problem.


Giving more complete information will give you a much better chance. 
It's not our job to be the family doctor and ask questions :-)


What GROMACS version is it? Does upgrading to 4.0.7 help?


While running the grompp (in both single and double precision) command I
get a Segmentation fault (core dumped) error.


When? What was the output to date?


The error persist even
after recompiling the GROMACS with gcc-4.4.3(previously I was running
4.04 compiled

Re: [gmx-users] grompp error(Segmentation fault)

[Arik Cohen]

Thank a lot for your very fast response !. Here are the requested details:

1. Version 4.07 is being used.

2. Upgrading from version 4.04 to 4.07 doesn't help.

3. The grompp command given is:

grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top 
-o 1bgq_Complex_b4ion..tpr


4. em.mdp:

integrator  =  l-bfgs
nsteps  =  5
nstlist =  1
rlist   =  1.0
coulombtype =  PME
rcoulomb=  1.0
vdw-type=  cut-off
rvdw=  1.0
nstenergy   =  10
emtol=  5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0
define  =  -DFLEXIBLE ; using flexible water model


5. The grompp command is issued in this case, before genion. However, 
even when running it alone the same problem arises.


6. The program is being run on Fedora 12 inside 
VMware(2.6.32.11-99.fc12.i686, 32-bit).


7. Running the same command on another OS and type of 
machine(fc10.x86_64) does not solve the problem


7. The output:

  :-)  G  R  O  M  A  C  S  (-:

 Gnomes, ROck Monsters And Chili Sauce

:-)  VERSION 4.0.7  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

 :-)  grompp_d (double precision)  (-:

Option Filename  Type Description

  -f MDP/em.mdp  Input, Opt!  grompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c 1bgq_Complex_b4ion.pdb  InputStructure file: gro g96 pdb 
tpr tpb

   tpa
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n  index.ndx  Input, Opt.  Index file
  -p 1bgq_Complex.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o 1bgq_Complex_b4ion..tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file: edr ene

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint0   Set the nicelevel
-[no]v   bool   yes Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
sites
-maxwarn int0   Number of allowed warnings during input 
processing

-[no]zerobool   no  Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum   bool   yes Renumber atomtypes and minimize number of
atomtypes

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...

WARNING 1 [file MDP/em.mdp, line unknown]:
  For efficient BFGS minimization, use switch/shift/pme instead of cut-off.

processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top//ffamber99sb.itp
Opening library file /usr/local/gromacs/share/gromacs/top//ffamber99sbnb.itp
Opening library file 
/usr/local/gromacs/share/gromacs/top//ffamber99sbbon.itp

Segmentation fault (core dumped)


Thanks a lot in advance for all your help

Arik


On 4/23/2010 4:45 PM, Mark Abraham wrote:

On 24/04/2010 7:28 AM, Arik Cohen wrote:

I'll be most thankful if any one would be able to help me with the
following problem.


Giving more complete information will give you a much better chance. 
It's not our job to be the family doctor and ask questions :-)


What GROMACS version is it? Does upgrading to 4.0.7 help?


While running the grompp (in both single and double precision) command I
get a Segmentation fault (core dumped) error.


When? What was the output to date?


The error persist even
after recompiling the GROMACS with gcc-4.4.3(previously I was running
4.04 compiled with the buggy gcc-4.1 compiler).


Does it happen on another machine?


The command I'm using is:

grompp_d -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top -o
1bgq.tpr


What's in the .mdp file?

Mark

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
P

Re: [gmx-users] grompp error(Segmentation fault)

[Mark Abraham]

On 24/04/2010 7:28 AM, Arik Cohen wrote:

I'll be most thankful if any one would be able to help me with the
following problem.


Giving more complete information will give you a much better chance. 
It's not our job to be the family doctor and ask questions :-)


What GROMACS version is it? Does upgrading to 4.0.7 help?


While running the grompp (in both single and double precision) command I
get a Segmentation fault (core dumped) error.


When? What was the output to date?


The error persist even
after recompiling the GROMACS with gcc-4.4.3(previously I was running
4.04 compiled with the buggy gcc-4.1 compiler).


Does it happen on another machine?


The command I'm using is:

grompp_d -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top -o
1bgq.tpr


What's in the .mdp file?

Mark
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[gmx-users] grompp error(Segmentation fault)

[Arik Cohen]

I'll be most thankful if any one would be able to help me with the 
following problem.


While running the grompp (in both single and double precision) command I 
get a Segmentation fault (core dumped) error. The error persist even 
after recompiling the GROMACS with gcc-4.4.3(previously I was running 
4.04 compiled with the buggy gcc-4.1 compiler).


The command I'm using is:

grompp_d -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top -o 
1bgq.tpr


Thanks

Arik


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