[gmx-developers] Gromos96 43a2 1-4 parameters
F.Hao at chem.rug.nl
F.Hao at chem.rug.nl
Tue Sep 2 10:11:15 CEST 2003
Hi, developers:
When I read the article from Lukas about G96 43a2 FF, I think
the parameters governing dihedral angle in aliphatic chain were
reconsidered. I only found he changed the parameters on one dihedral
and on 1-4 interactions involved CH2 and CH3. Is my understanding
correct? If so, however, the ffG43a2nb.itp file in gmx3.0 and gmx3.1
had changed not only for CH2-CH2, CH2-CH3 and CH3-CH3 but also
the 1-4 LJ in [ pairtypes ] between CH2, CH3 and other atomtypes.
Did these changes have influence in simulation compared to the old values
or any people had check it since Lukas didn't do parameterzation
between CH2 and N or other polar atomtypes in his paper?
Maybe I misunderstood something and I just want to make sure.
Thanks a lot in advance!
Best
Hao
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> 1. Re: gmx-users digest - Trajectory convert (lpgomes at procc.fiocruz.br)
> 2. Re: Re: gmx-users digest - Trajectory convert (Xavier Periole)
> 3. GROMACS and GCC on WinXP (TX)
> 4. Parameterising for a Solvent (Dallas Warren)
> 5. Re: Parameterising for a Solvent (Erik Lindahl)
> 6. Re: Parameterising for a Solvent (David)
> 7. Re: g_velacc again (Anton Feenstra)
> 8. Re: Gromacs Help (Anton Feenstra)
> 9. Re: Gromacs Help (Anton Feenstra)
> 10. Re: Parameterising for a Solvent (Dallas Warren)
>
> --__--__--
>
> Message: 1
> Date: Mon, 1 Sep 2003 19:26:35 -0000
> To: <gmx-users at gromacs.org>
> From: <lpgomes at procc.fiocruz.br>
> Subject: [gmx-users] Re: gmx-users digest - Trajectory convert
> Reply-To: gmx-users at gromacs.org
>
> HI all,
>
> I would like to know if there is some way for converting trajectories files to
> be read in InsightII program (or vice versa).
>
> Thanks in advance,
> Luciano P Gomes
> UNB/FIOCRUZ
>
> --__--__--
>
> Message: 2
> Date: Mon, 1 Sep 2003 09:08:24 -0400
> Subject: Re: [gmx-users] Re: gmx-users digest - Trajectory convert
> From: Xavier Periole <Xavier.Periole at physbio.mssm.edu>
> To: gmx-users at gromacs.org
> Reply-To: gmx-users at gromacs.org
>
>
>
> I think Insight reads g96 format. So you could convert your .xtc in
> the g96 format and hop !
>
> XAvier
>
>
> --__--__--
>
> Message: 3
> From: "TX" <xiet at rpi.edu>
> To: <gmx-users at gromacs.org>
> Date: Mon, 1 Sep 2003 18:14:53 -0400
> Subject: [gmx-users] GROMACS and GCC on WinXP
> Reply-To: gmx-users at gromacs.org
>
> Hi
> Has anyone successfully compiled GROMACS using GCC w/ MinGW? If so, what
> needs to be changed in the Makefile?
> Thanks,
>
>
> --__--__--
>
> Message: 4
> Date: Tue, 02 Sep 2003 12:21:56 +1000
> From: Dallas Warren <dallas.warren at vcp.monash.edu.au>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Parameterising for a Solvent
> Reply-To: gmx-users at gromacs.org
>
>
> --Boundary_(ID_lXwXzSzQQDUxEiPqLDsa+g)
> Content-type: text/plain; format=flowed; charset=us-ascii
> Content-transfer-encoding: 7BIT
>
> I am trying to get the parameters right for a solvent molecule.
>
> Appear to have the partial charges right, the dipole moment is within 0.25
> % (2.27 vs 2.276). Started with similar functional groups in the
> forcefield (G96 43a2x) and made some minor adjustments to get that close.
>
> Managed to get the density pretty good too, within 0.14 % (1035 vs
> 1036). Adjusted the value of L-J parameter V (Cij(6)) slightly to get this
> right.
>
> Problem is that the heat of vaporisation appears to be a long way off
> (-12.2 vs 58.0). To calculate this (I think this is correct ....), I took
> the internal energy from g_energy (26,545), divided by the number of
> molecules (1,800) to give 14.7 kJ/mol for the internal energy. Then
> subtracted this value from RT (2.47 kJ/mol), DHvap = -12.2.
>
> To get the correct value of DHvap the internal energy needs to be in the
> order of - 55 kJ/mol. This seems to be a large difference. Either I have
> calculated something incorrectly, are using the incorrect method, or the
> parameters are very wrong.
>
> If the former, then where did I go wrong?
>
> If the latter, then I guess I need to change V and W for the L-J potential
> such that the shape of the potential is similar (should preserve the
> density?) but the minimum energy is a fair amount larger (to decrease the
> value of 1-4 LJ and LJ SR enough)?
>
> Thank you for any comments.
>
> Catch ya,
>
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
> --------------------------------------------------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
>
> --Boundary_(ID_lXwXzSzQQDUxEiPqLDsa+g)
> Content-type: text/html; charset=us-ascii
> Content-transfer-encoding: 7BIT
>
> <html>
> I am trying to get the parameters right for a solvent molecule.<br><br>
> Appear to have the partial charges right, the dipole moment is within
> 0.25 % (2.27 vs 2.276). Started with similar functional groups in
> the forcefield (G96 43a2x) and made some minor adjustments to get that
> close.<br><br>
> Managed to get the density pretty good too, within 0.14 % (1035 vs
> 1036). Adjusted the value of L-J parameter V (Cij(6)) slightly to
> get this right.<br><br>
> Problem is that the heat of vaporisation appears to be a long way off
> (-12.2 vs 58.0). To calculate this (I think this is correct ....),
> I took the internal energy from g_energy (26,545), divided by the number
> of molecules (1,800) to give 14.7 kJ/mol for the internal energy.
> Then subtracted this value from RT (2.47 kJ/mol), DHvap =
> -12.2.<br><br>
> To get the correct value of DHvap the internal energy needs to be in the
> order of - 55 kJ/mol. This seems to be a large difference.
> Either I have calculated something incorrectly, are using the incorrect
> method, or the parameters are very wrong.<br><br>
> If the former, then where did I go wrong?<br><br>
> If the latter, then I guess I need to change V and W for the L-J
> potential such that the shape of the potential is similar (should
> preserve the density?) but the minimum energy is a fair amount larger (to
> decrease the value of 1-4 LJ and LJ SR enough)?<br><br>
> Thank you for any comments.<br><br>
> Catch ya,<br>
> <x-sigsep><p></x-sigsep>
> <b>Dr. Dallas Warren<br>
> </b><i>Research Fellow<br>
> </i>Department of Pharmaceutical Biology and Pharmacology<br>
> Victorian College of Pharmacy, Monash University<br>
> 381 Royal Parade, Parkville VIC 3010<br>
> <font color="#0000FF"><u>dallas.warren at vcp.monash.edu.au<br>
> </u></font>+61 3 9903 9083<br>
> <font face="Times New Roman, Times">--------------------------------------------------------------------------<br>
> <i>When the only tool you own is a hammer, every problem begins to
> resemble a nail.</font></i></html>
>
> --Boundary_(ID_lXwXzSzQQDUxEiPqLDsa+g)--
>
> --__--__--
>
> Message: 5
> Date: Mon, 1 Sep 2003 19:35:38 -0700
> Subject: Re: [gmx-users] Parameterising for a Solvent
> From: Erik Lindahl <lindahl at stanford.edu>
> To: gmx-users at gromacs.org
> Reply-To: gmx-users at gromacs.org
>
>
> --Apple-Mail-2-411076231
> Content-Transfer-Encoding: quoted-printable
> Content-Type: text/plain;
> delsp=yes;
> charset=ISO-8859-1;
> format=flowed
>
> Hi Dallas,
>
> To find the internal energy I would suggest running a single molecule =20=
>
> in vacuum.
>
> You will probably get a problem with sampling if it's a small molecule, =20=
>
> but that can be fixed by using langevin dynamics.
>
> You might also need to use double precision, and either shake with a =20
> small tolerance, or a lincs_order=3D8 to get very exact bond =
> constraining =20
> if you use that.
>
> Cheers,
>
> Erik
>
>
> On Monday, September 1, 2003, at 07:21 PM, Dallas Warren wrote:
>
> > I am trying to get the parameters right for a solvent molecule.
> >
> > Appear to have the partial charges right, the dipole moment is within =20=
>
> > 0.25 % (2.27 vs 2.276).=A0 Started with similar functional groups in =
> the =20
> > forcefield (G96 43a2x) and made some minor adjustments to get that =20
> > close.
> >
> > Managed to get the density pretty good too, within 0.14 % (1035 vs =20
> > 1036).=A0 Adjusted the value of L-J parameter V (Cij(6)) slightly to =
> get =20
> > this right.
> >
> > Problem is that the heat of vaporisation appears to be a long way off =20=
>
> > (-12.2 vs 58.0).=A0 To calculate this (I think this is correct ....), =
> I =20
> > took the internal energy from g_energy (26,545), divided by the number =
> =20
> > of molecules (1,800) to give 14.7 kJ/mol for the internal energy.=A0 =20=
>
> > Then subtracted this value from RT (2.47 kJ/mol), DHvap =3D -12.2.
> >
> > To get the correct value of DHvap the internal energy needs to be in =20=
>
> > the order of - 55 kJ/mol.=A0 This seems to be a large difference.=A0 =20=
>
> > Either I have calculated something incorrectly, are using the =20
> > incorrect method, or the parameters are very wrong.
> >
> > If the former, then where did I go wrong?
> >
> > If the latter, then I guess I need to change V and W for the L-J =20
> > potential such that the shape of the potential is similar (should =20
> > preserve the density?) but the minimum energy is a fair amount larger =20=
>
> > (to decrease the value of 1-4 LJ and LJ SR enough)?
> >
> > Thank you for any comments.
> >
> > Catch ya,
> >
> >
> >
> > Dr. Dallas Warren
> > Research Fellow
> > Department of Pharmaceutical Biology and Pharmacology
> > Victorian College of Pharmacy, Monash University
> > 381 Royal Parade, Parkville VIC 3010
> > dallas.warren at vcp.monash.edu.au
> > +61 3 9903 9083
> > =
> -----------------------------------------------------------------------=20=
>
> > ---
> > When the only tool you own is a hammer, every problem begins to =20
> > resemble a nail.
> >
>
> --Apple-Mail-2-411076231
> Content-Transfer-Encoding: quoted-printable
> Content-Type: text/enriched;
> charset=ISO-8859-1
>
> Hi Dallas,
>
>
> To find the internal energy I would suggest running a single molecule
> in vacuum.
>
>
> You will probably get a problem with sampling if it's a small
> molecule, but that can be fixed by using langevin dynamics.
>
>
> You might also need to use double precision, and either shake with a
> small tolerance, or a lincs_order=3D8 to get very exact bond
> constraining if you use that.
>
>
> Cheers,
>
>
> Erik
>
>
>
> On Monday, September 1, 2003, at 07:21 PM, Dallas Warren wrote:
>
>
> <excerpt>I am trying to get the parameters right for a solvent
> molecule.
>
>
> Appear to have the partial charges right, the dipole moment is within
> 0.25 % (2.27 vs 2.276).=A0 Started with similar functional groups in the
> forcefield (G96 43a2x) and made some minor adjustments to get that
> close.
>
>
> Managed to get the density pretty good too, within 0.14 % (1035 vs
> 1036).=A0 Adjusted the value of L-J parameter V (Cij(6)) slightly to get
> this right.
>
>
> Problem is that the heat of vaporisation appears to be a long way off
> (-12.2 vs 58.0).=A0 To calculate this (I think this is correct ....), I
> took the internal energy from g_energy (26,545), divided by the number
> of molecules (1,800) to give 14.7 kJ/mol for the internal energy.=A0
> Then subtracted this value from RT (2.47 kJ/mol), DHvap =3D -12.2.
>
>
> To get the correct value of DHvap the internal energy needs to be in
> the order of - 55 kJ/mol.=A0 This seems to be a large difference.=A0
> Either I have calculated something incorrectly, are using the
> incorrect method, or the parameters are very wrong.
>
>
> If the former, then where did I go wrong?
>
>
> If the latter, then I guess I need to change V and W for the L-J
> potential such that the shape of the potential is similar (should
> preserve the density?) but the minimum energy is a fair amount larger
> (to decrease the value of 1-4 LJ and LJ SR enough)?
>
>
> Thank you for any comments.
>
>
> Catch ya,
>
>
>
>
> <bold>Dr. Dallas Warren
>
> </bold><italic>Research Fellow
>
> </italic>Department of Pharmaceutical Biology and Pharmacology
>
> Victorian College of Pharmacy, Monash University
>
> 381 Royal Parade, Parkville VIC 3010
>
> =
> <underline><color><param>0000,0000,FFFF</param>dallas.warren at vcp.monash.ed=
> u.au
>
> </color></underline>+61 3 9903 9083
>
> <fontfamily><param>Times New =
> Roman</param>-------------------------------------------------------------=
> -------------
>
> <italic>When the only tool you own is a hammer, every problem begins
> to resemble a nail.</italic></fontfamily>
>
>
> </excerpt>=
>
> --Apple-Mail-2-411076231--
>
>
> --__--__--
>
> Message: 6
> Subject: Re: [gmx-users] Parameterising for a Solvent
> From: David <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Organization:
> Date: 02 Sep 2003 08:22:53 +0200
> Reply-To: gmx-users at gromacs.org
>
> On Tue, 2003-09-02 at 04:21, Dallas Warren wrote:
> > I am trying to get the parameters right for a solvent molecule.
> >
> > Appear to have the partial charges right, the dipole moment is within
> > 0.25 % (2.27 vs 2.276). Started with similar functional groups in the
> > forcefield (G96 43a2x) and made some minor adjustments to get that
> > close.
> >
> > Managed to get the density pretty good too, within 0.14 % (1035 vs
> > 1036). Adjusted the value of L-J parameter V (Cij(6)) slightly to get
> > this right.
> >
> > Problem is that the heat of vaporisation appears to be a long way off
> > (-12.2 vs 58.0). To calculate this (I think this is correct ....), I
> > took the internal energy from g_energy (26,545), divided by the number
> > of molecules (1,800) to give 14.7 kJ/mol for the internal energy.
> > Then subtracted this value from RT (2.47 kJ/mol), DHvap = -12.2.
> >
> > To get the correct value of DHvap the internal energy needs to be in
> > the order of - 55 kJ/mol. This seems to be a large difference.
> > Either I have calculated something incorrectly, are using the
> > incorrect method, or the parameters are very wrong.
> >
> > If the former, then where did I go wrong?
> DHvap = (Eintra(g) + RT) - (Eintra(l) + Einter(l))
> The second bit is your Epot in the liquid sim, then you have to compute
> Eintra(g) by running a simulation of a single molecule *IDENTICAL* to
> your liquid simulation. In particular when you use PME this will give a
> very large number. Take care to run the single molecule at least as long
> as the liquid simulation as you will have rather large fluctuations in
> energy. See further Wensink et al. (JCP 119, no 13, to be published).
>
> >
> > If the latter, then I guess I need to change V and W for the L-J
> > potential such that the shape of the potential is similar (should
> > preserve the density?) but the minimum energy is a fair amount larger
> > (to decrease the value of 1-4 LJ and LJ SR enough)?
> >
> > Thank you for any comments.
> >
> > Catch ya,
> >
> >
> > Dr. Dallas Warren
> > Research Fellow
> > Department of Pharmaceutical Biology and Pharmacology
> > Victorian College of Pharmacy, Monash University
> > 381 Royal Parade, Parkville VIC 3010
> > dallas.warren at vcp.monash.edu.au
> > +61 3 9903 9083
> > --------------------------------------------------------------------------
> > When the only tool you own is a hammer, every problem begins to
> > resemble a nail.
>
--
Best regards
Yours sincerely
Hao Fan :-)
-------------------------------------------------------------------------
Drs. Hao Fan email F.Hao at chem.rug.nl
Lab. of Biophysical Chemistry
University of Groningen
Nijenborgh 4 9747 AG GRONINGEN
The Netherlands
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