[gmx-users] genion
Shrivastava, Indira (NCI)
shrivasi at mail.nih.gov
Wed Sep 11 20:03:41 CEST 2002
-----Original Message-----
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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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