[gmx-users] RE: RE : FEP : separating components of dgdl (Berk Hess)
BON Michael
michael.bon at cea.fr
Wed Jan 30 11:59:30 CET 2008
Hi,
After some tedious work to locate the problem, I just realized that the term for bonds is missing in the log file !
It could account for the difference, but in fact another error occured :
(Note : I am using amber99 ports )
In my system, I defined an atom DUM with just the same parameters as H. When I do the transformation DUM->H, I have dVdl=0, which is OK.
If I change the parameters for bonds, that's to say in my .top file :
[ bondtypes ]
NC DUM 1 0.101 0;
NC H 1 0.101 363000;
(DUM and H are bound to a NC)
I still get dVdl = 0 ?! There should be a change due to this difference ( I did a run at lambda = 0.5 ) !
Moreover, when I cancel one of those two lines by adding a ";" at the beginning, I have an error message when using grompp saying "no default bond types..". So the program does not ignore those lines and needs them.
And if I change a parameter for angle, for example
[ angletypes ]
C NC DUM 1 120.00 0.
C NC H 1 120.00 400.
I do have a difference in dVdl
What is happening ?
Many thanks in advance,
Michael Bon
-------- Message d'origine--------
De: gmx-users-bounces at gromacs.org de la part de gmx-users-request at gromacs.org
Date: mar. 29/01/2008 16:00
À: gmx-users at gromacs.org
Objet : gmx-users Digest, Vol 45, Issue 119
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Today's Topics:
1. Re: gromacs versus amber boxsize -correction- (Mark Abraham)
2. Re: gromacs versus amber boxsize -correction- (Xavier Periole)
3. Re: gromacs versus amber boxsize (Xavier Periole)
4. Re: gromacs versus amber boxsize -correction- (Florian Haberl)
5. RE: RE : FEP : separating components of dgdl (Berk Hess)
6. chloroform - oplsaa (Mauro Puppett)
----------------------------------------------------------------------
Message: 1
Date: Tue, 29 Jan 2008 23:37:58 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] gromacs versus amber boxsize -correction-
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <479F1E26.6070304 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
servaas michielssens wrote:
> I made a mistake in the numbers, but the question remains:
>
> I ran the following command in gromacs:
> editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8
>
> The equivalent command in amber:
> solvateoct p61_vac.pdb TIP3PBOX 8.0
>
> As far as I understand this, both command created a box were the edges
> are 0.8 nm away from the solute. But the resulting image distance (d in
> the manual) in gromacs is:
> 121.3092
> and in amber:
> 110.5103716
What shapes were these commands creating? How are you measuring this
image distance?
Mark
------------------------------
Message: 2
Date: Tue, 29 Jan 2008 13:35:07 +0100
From: "Xavier Periole" <X.Periole at rug.nl>
Subject: Re: [gmx-users] gromacs versus amber boxsize -correction-
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <web-65356876 at mail3.rug.nl>
Content-Type: text/plain;charset=utf-8;format="flowed"
On Tue, 29 Jan 2008 13:14:21 +0100
"servaas michielssens" <servaas.michielssens at student.kuleuven.be> wrote:
> I made a mistake in the numbers, but the question remains:
>
> I ran the following command in gromacs:
> editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8
>
> The equivalent command in amber:
> solvateoct p61_vac.pdb TIP3PBOX 8.0
is there any reorientation in volved?
> As far as I understand this, both command created a box were the edges are
>0.8 nm away from the solute. But the resulting image distance (d in the
>manual)
amber or gromacs manual?
> in gromacs is:
> 121.3092
> and in amber:
> 110.5103716
Are the d the same in both programs?
The definitions of dodecahedron are different in gromacs and gromos.
could be a similar problem in with amber!
Note however that the gromacs definition decreased the volume as
compared to gromos.
>
> This is makes a hugde difference in the number of water atoms to add.
> Does anyone has an explanation for this paradox?
>
>
> kind regards,
>
> servaas
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
------------------------------
Message: 3
Date: Tue, 29 Jan 2008 13:37:59 +0100
From: "Xavier Periole" <X.Periole at rug.nl>
Subject: Re: [gmx-users] gromacs versus amber boxsize
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <web-65357185 at mail3.rug.nl>
Content-Type: text/plain;charset=utf-8;format="flowed"
On Tue, 29 Jan 2008 12:57:13 +0100
"servaas michielssens" <servaas.michielssens at student.kuleuven.be> wrote:
> I ran the following command in gromacs:
> editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8
>
> The equivalent command in amber:
> solvateoct p61_vac.pdb TIP3PBOX 8.0
>
> As far as I understand this, both command created a box were the edges are
>0.8 nm away from the solute. But the resulting image distance (d in the
>manual) in gromacs is:
> 121.3092
> and in amber:
> 85.9385483
the box size is changing that fast? Which one is the right value?
>
> This is makes a hugde difference in the number of water atoms to add.
> Does anyone has an explanation for this paradox?
>
>
> kind regards,
>
> servaas
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
------------------------------
Message: 4
Date: Tue, 29 Jan 2008 13:43:13 +0100
From: Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de>
Subject: Re: [gmx-users] gromacs versus amber boxsize -correction-
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <200801291343.14603.Florian.Haberl at chemie.uni-erlangen.de>
Content-Type: text/plain; charset="utf-8"
Hi,
On Tuesday, 29. January 2008 13:14, servaas michielssens wrote:
> I made a mistake in the numbers, but the question remains:
>
> I ran the following command in gromacs:
> editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8
With -d and a triclinic box the size of the system in the x, y and z
directions is used. With -d and cubic, dodecahedron or octahedron boxes, the
dimensions are set to the diameter of the system (largest distance between
atoms) plus twice the specified distance. [from editconf -h]
>
> The equivalent command in amber:
> solvateoct p61_vac.pdb TIP3PBOX 8.0
generates a truncated octahedron periodic box
>
> As far as I understand this, both command created a box were the edges are
> 0.8 nm away from the solute. But the resulting image distance (d in the
> manual) in gromacs is: 121.3092
> and in amber:
> 110.5103716
>
> This is makes a hugde difference in the number of water atoms to add.
> Does anyone has an explanation for this paradox?
so you generate two different boxsizes or types.
>
>
> kind regards,
>
> servaas
greetings,
Florian
--
-------------------------------------------------------------------------------
Florian Haberl
Computer-Chemie-Centrum
Universitaet Erlangen/ Nuernberg
Naegelsbachstr 25
D-91052 Erlangen
Telephone: +49(0) â^' 9131 â^' 85 26573
Mailto: florian.haberl AT chemie.uni-erlangen.de
-------------------------------------------------------------------------------
------------------------------
Message: 5
Date: Tue, 29 Jan 2008 15:08:31 +0100
From: Berk Hess <gmx3 at hotmail.com>
Subject: [gmx-users] RE: RE : FEP : separating components of dgdl
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <BLU134-W269C3D885A8C90EABEC0F78E350 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
I overlooked that you printed dVdl, not dGdl.
Without looking into the code, I would not know where term is missing.
Can you figure out if any energy terms are missing in the print?
Please check if all energy terms in de log file are present in the dvdl print.
I would guess that the dvdl numbers are correct, but there could be a mistake
in there as well.
Selectively turning off perturbations would find it, but that is a bit of work.
Berk.
> It is a single processor simulation.
>
> As I change some masses,I have indeed a change in Ekin (-1,23e+00) , but it should not explain what happens with Vpot, should it ?
> I also have position restraints whose parameters do not change, so dVdl should be 0, which is what it reads. I did
> not copy this in my previous mail, I should have.
>
> Thanks for your help,
> Michael Bon
>
>
> -------- Message d'origine--------
> De: gmx-users-bounces at gromacs.org de la part de gmx-users-request at gromacs.org
> Date: mar. 29/01/2008 12:00
> À: gmx-users at gromacs.org
> Objet : gmx-users Digest, Vol 45, Issue 116
>
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
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>
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Re: dihedral restraints wiki section (Behnoush Zare)
> 2. RE : FEP : separating components of dgdl (BON Michael)
> 3. RE: RE : FEP : separating components of dgdl (Berk Hess)
> 4. Re: dihedral restraints wiki section (Xavier Periole)
> 5. Re: GROMACS ON CYGWIN. (Nabajyoti Goswami)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 29 Jan 2008 13:06:14 +0330 (IRST)
> From: Behnoush Zare <bzare at iums.ac.ir>
> Subject: Re: [gmx-users] dihedral restraints wiki section
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <26532812.27691201599374219.JavaMail.root at zimbra.iums.ac.ir>
> Content-Type: text/plain; charset=utf-8
>
> Dear chris,
>
> Thank you for your help about performing dihedral restraints. Would you please kindly explain to me how I can measure the value of dihedral angles between two amin acids (I mean C'-N-C-C' and N-C-C'-N).
> Thank you in advance for your valuable aid.
>
> Behnoush
>
> ----- Original Message -----
> From: "chris neale" <chris.neale at utoronto.ca>
> To: gmx-users at gromacs.org
> Sent: Sunday, January 27, 2008 11:49:42 PM (GMT+0330) Asia/Tehran
> Subject: [gmx-users] dihedral restraints wiki section
>
> I have added a section on dihedral restraints to the wiki.
>
> http://wiki.gromacs.org/index.php/Dihedral_Restraints
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.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 to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 29 Jan 2008 10:24:57 +0100
> From: "BON Michael" <michael.bon at cea.fr>
> Subject: [gmx-users] RE : FEP : separating components of dgdl
> To: <gmx-users at gromacs.org>
> Message-ID:
> <92F41516EE90B540BC03B8C4613EF6B933CC72 at DIODON.extra.cea.fr>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Thanks for the quick reply.
>
> I have an other question : I ran a quick simulation on a single node using mdrun -sepdvdl and the components are written in
> the .log file. But the final value of dVpot/dlambda doesn't seem to be the sum of the components above. Example for some step:
>
> VdW and Coulomb SR : dVdl -2.72859e+02
> Angle : dVdl 3.56537e+00
> Proper Dih. : dVdl -7.31260e-03
> Ryckaert-Bell. : dVdl -1.13654e-01
> LJ-14 + Coulomb-14 : dVdl 6.39499e+02
> Dispersion correc. : dVdl 0.00000e+00
>
> And I read : dVpot/dlambda = 3.62310e+02, instead of 3.70e+02.
>
> There is no PME in this sim.
>
> What did I forget ?
>
> Many thanks in advance,
>
> Michaël Bon
> -------------- next part --------------
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> ------------------------------
>
> Message: 3
> Date: Tue, 29 Jan 2008 10:32:08 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: [gmx-users] RE: RE : FEP : separating components of dgdl
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BLU134-W229F0850B9736B358C55858E350 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
>
> ----------------------------------------
> > Date: Tue, 29 Jan 2008 10:24:57 +0100
> > From: michael.bon at cea.fr
> > To: gmx-users at gromacs.org
> > Subject: RE : FEP : separating components of dgdl
> >
> >
> > Thanks for the quick reply.
> >
> > I have an other question : I ran a quick simulation on a single node using mdrun -sepdvdl and the components are written in
> > the .log file. But the final value of dVpot/dlambda doesn't seem to be the sum of the components above. Example for some step:
> >
> > VdW and Coulomb SR : dVdl -2.72859e+02
> > Angle : dVdl 3.56537e+00
> > Proper Dih. : dVdl -7.31260e-03
> > Ryckaert-Bell. : dVdl -1.13654e-01
> > LJ-14 + Coulomb-14 : dVdl 6.39499e+02
> > Dispersion correc. : dVdl 0.00000e+00
> >
> > And I read : dVpot/dlambda = 3.62310e+02, instead of 3.70e+02.
> >
> > There is no PME in this sim.
> >
> > What did I forget ?
>
> I assume you are running single processor.
> The terms are per processor.
>
> I think that the only contributions that are no added are:
> constraints, only when you change constraint lengths,
> kinetic energy, only when you change masses.
>
> So do you change constraint lengths or masses?
>
> Berk.
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's FREE!
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> ------------------------------
>
> Message: 4
> Date: Tue, 29 Jan 2008 10:47:45 +0100
> From: "Xavier Periole" <X.Periole at rug.nl>
> Subject: Re: [gmx-users] dihedral restraints wiki section
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <web-65336809 at mail3.rug.nl>
> Content-Type: text/plain;charset=utf-8;format="flowed"
>
>
>
> > Thank you for your help about performing dihedral restraints. Would you
> >please kindly explain to me how I can measure the value of dihedral angles
> >between two amin acids (I mean C'-N-C-C' and N-C-C'-N).
> > Thank you in advance for your valuable aid.
>
> Well this should really be easy to find out! check out the manual,
> there is section ANALYSIS ... g_angle is one option.
>
> >
> > Behnoush
> >
> > ----- Original Message -----
> >From: "chris neale" <chris.neale at utoronto.ca>
> > To: gmx-users at gromacs.org
> > Sent: Sunday, January 27, 2008 11:49:42 PM (GMT+0330) Asia/Tehran
> > Subject: [gmx-users] dihedral restraints wiki section
> >
> > I have added a section on dihedral restraints to the wiki.
> >
> > http://wiki.gromacs.org/index.php/Dihedral_Restraints
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.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 to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.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 to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> -----------------------------------------------------
> XAvier Periole - PhD
>
> NMR & Molecular Dynamics Group
> University of Groningen
> The Netherlands
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 29 Jan 2008 15:21:37 +0530
> From: "Nabajyoti Goswami" <nabajyoti.goswami at gmail.com>
> Subject: Re: [gmx-users] GROMACS ON CYGWIN.
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <e14f21f70801290151y7f59cd6fq9539d1a509836e68 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> If you are in windows and want to use gromacs by cygwin I suggest you to use
> the window version of gromacs. place all gromacs executable into
> C:/cygwin/home/bin *or* C:/windows/system32. It must work.
>
> On Jan 28, 2008 8:29 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> > DAVID RINCON wrote:
> > > Good morning people,
> > >
> > > I want to install gromacs on my laptop and I have installed cygwin and
> > > some necessery gromacs libraries as fftw. But, when I am going to
> > install,
> > >
> > > glibc
> > >
> > > just in the first step with ./configure. That broke down. :S
> >
> > Imagine I rang my car mechanic and told him that the car was borken and
> > the spare tyre was making a weird noise, and asked him what was wrong...
> > He'd ask me to bring him the car or describe the problem better. :-)
> >
> > > Someone has installed gromacs on their computers?
> > > How can I do it?
> >
> > Start here http://wiki.gromacs.org/index.php/GROMACS_on_Windows and
> > check out the general advice here
> > http://www.catb.org/~esr/faqs/smart-questions.html<http://www.catb.org/%7Eesr/faqs/smart-questions.html>
> >
> > Mark
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.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 to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> Regads,
> Nabajyoti Goswami
>
>
>
>
>
>
>
>
>
>
>
>
> Ph.D Student.
> Center for Biotechnology,
> Anna University,
> Chennai-600025
> Tamil Nadu.
> Mobile: 09840487093
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>
> End of gmx-users Digest, Vol 45, Issue 116
> ******************************************
>
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Message: 6
Date: Tue, 29 Jan 2008 15:47:07 +0100
From: Mauro Puppett <esagono at hotmail.com>
Subject: [gmx-users] chloroform - oplsaa
To: <gmx-users at gromacs.org>
Message-ID: <BLU110-W59ABF292F2C6FA5AF97DB6B1350 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi all,
I'm trying to run a simulation of a phenol in chloroform with the oplsaa forcefield.
I've downloaded the chloroform box from gromacs and added the files to the top folder.
Everything is fine till I run grompp which says:
Fatal error:
Invalid order for directive atomtypes, file ""/usr/local/gromacs/share/gromacs/top/chcl3.itp"", line 1
After downloading the chcl3 box should i have to modify something else?
I've checked in the manual but I'm not able to understand what i'm doing wrong.
This is the top file of my phenol I get after running pdb2gmx:
;
; File 'fenolo.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Fri Jan 25 15:47:30 2008
;
; This is your topology file
; "Ramones For Ever" (P.J. Van Maaren)
;
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 opls_145 1 FEN CG 1 -0.193 12.011 ; qtot -0.193
2 opls_145 1 FEN CD2 2 -0.1642 12.011 ; qtot -0.3572
3 opls_145 1 FEN CE2 3 -0.3176 12.011 ; qtot -0.6748
4 opls_166 1 FEN CZ 4 0.5484 12.011 ; qtot -0.1264
5 opls_145 1 FEN CE1 5 -0.3953 12.011 ; qtot -0.5217
6 opls_145 1 FEN CD1 6 -0.0852 12.011 ; qtot -0.6069
7 opls_146 1 FEN HD2 7 0.171 1.008 ; qtot -0.4359
8 opls_146 1 FEN HE1 8 0.163 1.008 ; qtot -0.2729
9 opls_146 1 FEN HE2 9 0.1907 1.008 ; qtot -0.0822
10 opls_146 1 FEN HD1 10 0.1506 1.008 ; qtot 0.0684
11 opls_146 1 FEN HG 11 0.1496 1.008 ; qtot 0.218
12 opls_167 1 FEN OH 12 -0.6515 15.9994 ; qtot -0.4335
13 opls_168 1 FEN HH 13 0.4334 1.008 ; qtot -0.0001
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 6 1
1 11 1
2 3 1
2 7 1
3 4 1
3 9 1
4 5 1
4 12 1
5 6 1
5 8 1
6 10 1
12 13 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 8 1
1 9 1
2 5 1
2 10 1
2 12 1
3 6 1
3 8 1
3 11 1
3 13 1
4 7 1
4 10 1
5 9 1
5 11 1
5 13 1
6 7 1
6 12 1
7 9 1
7 11 1
8 10 1
8 12 1
9 12 1
10 11 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 6 1
2 1 11 1
6 1 11 1
1 2 3 1
1 2 7 1
3 2 7 1
2 3 4 1
2 3 9 1
4 3 9 1
3 4 5 1
3 4 12 1
5 4 12 1
4 5 6 1
4 5 8 1
6 5 8 1
1 6 5 1
1 6 10 1
5 6 10 1
4 12 13 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
6 1 2 3 3
6 1 2 7 3
11 1 2 3 3
11 1 2 7 3
2 1 6 5 3
2 1 6 10 3
11 1 6 5 3
11 1 6 10 3
1 2 3 4 3
1 2 3 9 3
7 2 3 4 3
7 2 3 9 3
2 3 4 5 3
2 3 4 12 3
9 3 4 5 3
9 3 4 12 3
3 4 5 6 3
3 4 5 8 3
12 4 5 6 3
12 4 5 8 3
3 4 12 13 3
5 4 12 13 3
4 5 6 1 3
4 5 6 10 3
8 5 6 1 3
8 5 6 10 3
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "chcl3.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
fenolo in chcl3
[ molecules ]
; Compound #mols
Protein 1
Thanks in advance
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End of gmx-users Digest, Vol 45, Issue 119
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