[gmx-users] genion

Shrivastava, Indira (NCI) shrivasi at mail.nih.gov
Wed Sep 11 20:03:41 CEST 2002



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Today's Topics:

   1. GROMOS96 topology (Ruben Martinez Buey)
   2. Re: GROMOS96 topology (Daan Virtual)
   3. Fatal error Determinant (Mehmet Suezen)
   4. Re: Fatal error Determinant (Mehmet Suezen)
   5. Re: Fatal error Determinant (David van der Spoel)
   6. Re: Fatal error Determinant (Mehmet Suezen)
   7. Re: Fatal error Determinant (David van der Spoel)
   8. Re: Fatal error Determinant (Nguyen Hoang Phuong)
   9. Re: Fatal error Determinant (Mehmet Suezen)
  10. Re: Fatal error Determinant (David van der Spoel)
  11. Fatal error Determinant (Mehmet Suezen)
  12. Re: Fatal error Determinant (David van der Spoel)
  13. Re: Fatal error Determinant (Mehmet Suezen)
  14. genion (storme at rpi.edu)

--__--__--

Message: 1
Date: Wed, 11 Sep 2002 21:33:54 +0200
From: Ruben Martinez Buey <ruben at akilonia.cib.csic.es>
Organization: CIB-CSIC
To: gmx-users at gromacs.org
Subject: [gmx-users] GROMOS96 topology

Hi all,
I have a small molecule with more than 100 atoms/bonds/angles. When
PRODRG generates the GROMOS87 topology, an error occurs:
_____________________________
29
DRG
6672**3038 0 0 1 1 1 1
______________________________________________________________________

I want to use GROMOS96, so I would like to generate a molecular topology
for GROMOS87 with PRODRG
and convert to GROMOS96 with the program "cnvtop.64" included in the
GROMOS96 software.
Can anyone help me?
Thanks a lot for your help
with best regards
Ruben
___________________________________________

Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144  28006  MADRID
Tlf: +34-91-561 18 00 ext. 4380
___________________________________________



--__--__--

Message: 2
Date: Wed, 11 Sep 2002 09:35:36 +0100 (BST)
From: Daan Virtual <vdava at davapc1.bioch.dundee.ac.uk>
To: Ruben Martinez Buey <ruben at akilonia.cib.csic.es>
cc: <gmx-users at gromacs.org>
Subject: Re: [gmx-users] GROMOS96 topology


Hi Ruben

The problem here is that for historical reasons GROMOS87 is limited to a
maximum of 99 atoms, bonds, angles etc. This is simply because there is
only a two-character space for these parameters in the topology.
Therefore, originally PRODRG could also only deal with < 100 atoms. This
limitation has now been removed but it does mean that the GROMOS87 output
produced with > 100 atoms (or indeed > 100 bonds, angles etc.) contains
rubbish (the ** in your file). This problem as such cannot be solved.

However, I am quite willing to incorporate GROMOS96 format in PRODRG
directly if somebody on this list con provide me with a full set of
installation files and a manual.

cheers

Daan

On Wed, 11 Sep 2002, Ruben Martinez Buey wrote:

> Hi all,
> I have a small molecule with more than 100 atoms/bonds/angles. When
> PRODRG generates the GROMOS87 topology, an error occurs:
> _____________________________
> 29
> DRG
> 6672**3038 0 0 1 1 1 1
> ______________________________________________________________________
>
> I want to use GROMOS96, so I would like to generate a molecular topology
> for GROMOS87 with PRODRG
> and convert to GROMOS96 with the program "cnvtop.64" included in the
> GROMOS96 software.
> Can anyone help me?
> Thanks a lot for your help
> with best regards
> Ruben
> ___________________________________________
>
> Rub=E9n Mart=EDnez-Buey. PhD student
> Protein Function and Structure Dept. Lab. 352
> Centro de Investigaciones Biol=F3gicas (CIB-CSIC)
> C/ Vel=E1zquez, 144  28006  MADRID
> Tlf: +34-91-561 18 00 ext. 4380
> ___________________________________________
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>


###########################################################################=
###

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac=
=2Euk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.=
uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies=
!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk=
/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.htm=
l
       "
       O


--__--__--

Message: 3
Date: Wed, 11 Sep 2002 15:53:03 +0200
From: Mehmet Suezen <suzen at theochem.tu-muenchen.de>
Organization: TU Muenchen
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] Fatal error Determinant

Dear Gromacs Users,

Anybody ever obtained Fatal error: Determinant after running mdrun.
as;
Fatal error: Determinant =
1201087450187478402970099969957581291520.000000

Why this huge number occured ? Is is related to Inertia Tensor?

Cheers, Mehmet

--__--__--

Message: 4
Date: Wed, 11 Sep 2002 15:57:54 +0200
From: Mehmet Suezen <suzen at theochem.tu-muenchen.de>
Organization: TU Muenchen
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Fatal error Determinant

Mehmet Suezen wrote:
> 
> Dear Gromacs Users,
> 
> Anybody ever obtained Fatal error: Determinant after running mdrun.
> as;
> Fatal error: Determinant =
> 1201087450187478402970099969957581291520.000000
> 
> Why this huge number occured ? Is is related to Inertia Tensor?

Let me reply my self:) Bad initial structure! 
http://www.gromacs.org/pipermail/gmx-users/2001-December/000301.html

But any other suggestion would be appreciated.

Cheers,Mehmet

--__--__--

Message: 5
Subject: Re: [gmx-users] Fatal error Determinant
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Mehmet Suezen <suzen at theochem.tu-muenchen.de>
Cc: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Date: 11 Sep 2002 16:06:20 +0200


On Wed, 2002-09-11 at 15:53, Mehmet Suezen wrote:
> Dear Gromacs Users,
> 
> Anybody ever obtained Fatal error: Determinant after running mdrun.
> as;
> Fatal error: Determinant =
> 1201087450187478402970099969957581291520.000000
> 
> Why this huge number occured ? Is is related to Inertia Tensor?

removing rotation about center of mass motion with reasonably old
gromacs?

> 
> Cheers, Mehmet
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

--__--__--

Message: 6
Date: Wed, 11 Sep 2002 16:19:37 +0200
From: Mehmet Suezen <suzen at theochem.tu-muenchen.de>
Organization: TU Muenchen
To: David van der Spoel <spoel at xray.bmc.uu.se>
CC: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Fatal error Determinant

David van der Spoel wrote:
> 
> about center of mass motion with reasonably old
> gromacs?

Error occured with gromacs3.1.3 and nstcomm=-1. It is strange because
I can used same set up with different number of particles.(different
geometry)

cheers, Mehmet

--__--__--

Message: 7
Subject: Re: [gmx-users] Fatal error Determinant
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Mehmet Suezen <suzen at theochem.tu-muenchen.de>
Cc: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Date: 11 Sep 2002 16:23:33 +0200

On Wed, 2002-09-11 at 16:19, Mehmet Suezen wrote:
> David van der Spoel wrote:
> > 
> > about center of mass motion with reasonably old
> > gromacs?
> 
> Error occured with gromacs3.1.3 and nstcomm=-1. It is strange because
> I can used same set up with different number of particles.(different
> geometry)
could it be that the particles are all in a plane? Then the algorithm
won't work...
> 
> cheers, Mehmet
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

--__--__--

Message: 8
Date: Wed, 11 Sep 2002 16:41:50 +0200 (MEST)
From: Nguyen Hoang Phuong <phuong at theochem.uni-frankfurt.de>
To: David van der Spoel <spoel at xray.bmc.uu.se>
cc: Mehmet Suezen <suzen at theochem.tu-muenchen.de>, 
    "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Fatal error Determinant


On 11 Sep 2002, David van der Spoel wrote:

> On Wed, 2002-09-11 at 16:19, Mehmet Suezen wrote:
> > David van der Spoel wrote:
> > > 
> > > about center of mass motion with reasonably old
> > > gromacs?
> > 
> > Error occured with gromacs3.1.3 and nstcomm=-1. It is strange because
> > I can used same set up with different number of particles.(different
> > geometry)
> could it be that the particles are all in a plane? Then the algorithm
> won't work...
> > 

this is correct. I had the same problem with my planar molecule.

Phuong
-----
> > cheers, Mehmet
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > 
> -- 
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 


--__--__--

Message: 9
Date: Wed, 11 Sep 2002 16:51:18 +0200
From: Mehmet Suezen <suzen at theochem.tu-muenchen.de>
Organization: TU Muenchen
To: David van der Spoel <spoel at xray.bmc.uu.se>
CC: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Fatal error Determinant

David van der Spoel wrote:
> 
> On Wed, 2002-09-11 at 16:19, Mehmet Suezen wrote:
> > David van der Spoel wrote:
> > >
> > > about center of mass motion with reasonably old
> > > gromacs?
> >
> > Error occured with gromacs3.1.3 and nstcomm=-1. It is strange because
> > I can used same set up with different number of particles.(different
> > geometry)
> could it be that the particles are all in a plane? Then the algorithm
> won't work...
> >

It is a random structure and when I produce tpr grommp also complains

WARNING 2 [file sample.mdp, line unknown]:
mdrun will apply removal of angular momentum when nstcomm < 0
checking input for internal consistency...

even nstcomm is -1. I can run it for a single step but more is trouble.

cheers, Mehmet

> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel,        Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,          75123 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

--__--__--

Message: 10
Subject: Re: [gmx-users] Fatal error Determinant
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Mehmet Suezen <suzen at theochem.tu-muenchen.de>
Cc: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Date: 11 Sep 2002 17:04:45 +0200

On Wed, 2002-09-11 at 16:51, Mehmet Suezen wrote:
> David van der Spoel wrote:
> > 
> > On Wed, 2002-09-11 at 16:19, Mehmet Suezen wrote:
> > > David van der Spoel wrote:
> > > >
> > > > about center of mass motion with reasonably old
> > > > gromacs?
> > >
> > > Error occured with gromacs3.1.3 and nstcomm=-1. It is strange because
> > > I can used same set up with different number of particles.(different
> > > geometry)
> > could it be that the particles are all in a plane? Then the algorithm
> > won't work...
> > >
> 
> It is a random structure and when I produce tpr grommp also complains
> 
> WARNING 2 [file sample.mdp, line unknown]:
> mdrun will apply removal of angular momentum when nstcomm < 0
> checking input for internal consistency...
> 
> even nstcomm is -1. I can run it for a single step but more is trouble.
Have you checked the coordinates after 1 step? Are they NaN or inf?
> 
> cheers, Mehmet
> 
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > >
> > --
> > Groeten, David.
> > ________________________________________________________________________
> > Dr. David van der Spoel,        Biomedical center, Dept. of Biochemistry
> > Husargatan 3, Box 576,          75123 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

--__--__--

Message: 11
Date: Wed, 11 Sep 2002 17:29:14 +0200
From: Mehmet Suezen <suzen at theochem.tu-muenchen.de>
Organization: TU Muenchen
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] Fatal error Determinant

> David van der Spoel wrote:
> 
> > Have you checked the coordinates after 1 step? Are they NaN or inf?
It is normal, non of them. Actually problem arrises some where between
10 -100 steps. Unusally,
program do not predict finish timing
 
cheers,mehmet

--__--__--

Message: 12
Subject: Re: [gmx-users] Fatal error Determinant
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Mehmet Suezen <suzen at theochem.tu-muenchen.de>
Cc: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Date: 11 Sep 2002 17:38:14 +0200

On Wed, 2002-09-11 at 17:29, Mehmet Suezen wrote:
> > David van der Spoel wrote:
> > 
> > > Have you checked the coordinates after 1 step? Are they NaN or inf?
> It is normal, non of them. Actually problem arrises some where between
> 10 -100 steps. Unusally,
> program do not predict finish timing
it's still most likely the physics: exploding system or something like
that...

>  
> cheers,mehmet
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

--__--__--

Message: 13
Date: Wed, 11 Sep 2002 18:44:29 +0200
From: Mehmet Suezen <suzen at theochem.tu-muenchen.de>
Organization: TU Muenchen
To: David van der Spoel <spoel at xray.bmc.uu.se>
CC: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Fatal error Determinant

David van der Spoel wrote:
> 
> On Wed, 2002-09-11 at 17:29, Mehmet Suezen wrote:
> > > David van der Spoel wrote:
> > >
> > > > Have you checked the coordinates after 1 step? Are they NaN or inf?
> > It is normal, non of them. Actually problem arrises some where between
> > 10 -100 steps. Unusally,
> > program do not predict finish timing
> it's still most likely the physics: exploding system or something like
> that...

basicly I've merged two equilibrium geometries. Single geometry works
perfectly, unlike
merged one. If I continue to remove angular motion system gives
mentioned error.
Really, I didn't get why?
cheers,mehmet
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel,        Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,          75123 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

--__--__--

Message: 14
To: gmx-users at gromacs.org
From: storme at rpi.edu
Reply-To: storme at rpi.edu
Date: Wed, 11 Sep 2002 13:47:07 EDT
Subject: [gmx-users] genion

Hi All,
	I'm trying to use genion to insert 7 Na counter ions into a protein
simulation. I use the following command line.

	genion -s md.tpr -np 7 -pq 1 -o withNa.gro

This works as it should and replaces 7 water molecules with Na. I then fix
the topology file by subtracting 7 from the number of solvent molecules and
add 7 Na molecules. I also add ions.itp. The problem occurs when I try to
run these new .gro and .top files through grompp. I get the error:

Fatal error: No such moleculetype Na

This error seems a little strange since the molecule type Na is define in
ions.itp. Let me know if you can tell what I'm doing wrong. Thanks Alot.
						
Erik Storm					



--__--__--

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users


Try creating a separate itp file for Na ions only, and include that in your 
topology file. That should work. 

best wishes
Indira 

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