[gmx-users] Re: Molecular volume
David Mobley
dmobley at gmail.com
Tue Nov 7 01:02:10 CET 2006
Mohan,
This following excerpt was on the gmx-revision list in July. You
probably need the CVS version of 3.3 to take advantage of this option:
I've used it myself, with that version. Seems to work fine.
>Added a new option to g_sas in order to compute the volume and density
>of a sample. The volume was already computed by the double-cube lattice
>method but we never used the result. Option is -tv.
>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: 46 18 471 4205 fax: 46 18 511 755
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>_______________________________________________
>gmx-revision mailing list
>gmx-revision at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-revision
On 11/6/06, Mohan Boggara <mohanbabu.boggara at gmail.com> wrote:
> Hi David,
> Thanks for you reply, g_sas gives solvent accesible surface area but not the
> volume. In any case, that might be of some help.
> Thanks
> Mohan
>
> On 06/11/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
> wrote:
> > 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
> > gmx-users-request at gromacs.org
> >
> > You can reach the person managing the list at
> > gmx-users-owner at gromacs.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Atom q2 not found in rtp database in residue TRP (Joern Lenz)
> > 2. Re: Atom q2 not found in rtp database in residue TRP
> > (David van der Spoel)
> > 3. Smooth surface (Alexei Krukau)
> > 4. Re: Atom q2 not found in rtp database in residue TRP (Joern Lenz)
> > 5. Re: Fw: gmx-3.3.1_cpmd-3.11.1 with mpirun (Pradip K Biswas)
> > 6. Re: (dH/dl) calculation (David Mobley)
> > 7. Molecular volume (Mohan Boggara)
> > 8. Re: Molecular volume (David Mobley)
> >
> >
> >
> ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 6 Nov 2006 12:03:33 +0100
> > From: Joern Lenz < JLenz at zbh.uni-hamburg.de>
> > Subject: [gmx-users] Atom q2 not found in rtp database in residue TRP
> > To: gmx-users at gromacs.org
> > Message-ID: <
> 200611061203.33366.JLenz at zbh.uni-hamburg.de>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > dear gromacs users,
> >
> > i am performing a simulation of a system of a protein together with a DNA
> > using the amber03 forcefield which i loaded down from
> > http://folding.stanford.edu/AMBER.html.
> > I converted all LYS residues in my pdb file into LYP and all HIS into HIP
> > (please correct me if you think that this does not make sense).
> > Does anyone know a script or program which automatically converts pdb
> files
> > into amber pdb files so that i can use the amber03 FF without changing
> atoms
> > here and there ?
> >
> > QUESTION:
> > When i start pdb2gmx there always occurs the same error:
> > "Atom q2 not found in rtp database in residue TRP"
> > I cannot recognize where this error comes from and so i am not able to fix
> > this error.
> > Has anyone got an idea ?
> > Thanks a lot and have a nice day using gromacs
> > greeting
> > joern
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 06 Nov 2006 13:39:23 +0100
> > From: David van der Spoel < spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] Atom q2 not found in rtp database in residue
> > TRP
> > To: Discussion list for GROMACS users < gmx-users at gromacs.org>
> > Message-ID: <454F2CFB.3050505 at xray.bmc.uu.se>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Joern Lenz wrote:
> > > dear gromacs users,
> > >
> > > i am performing a simulation of a system of a protein together with a
> DNA
> > > using the amber03 forcefield which i loaded down from
> > > http://folding.stanford.edu/AMBER.html.
> > > I converted all LYS residues in my pdb file into LYP and all HIS into
> HIP
> > > (please correct me if you think that this does not make sense).
> > > Does anyone know a script or program which automatically converts pdb
> files
> > > into amber pdb files so that i can use the amber03 FF without changing
> atoms
> > > here and there ?
> > >
> > > QUESTION:
> > > When i start pdb2gmx there always occurs the same error:
> > > "Atom q2 not found in rtp database in residue TRP"
> > > I cannot recognize where this error comes from and so i am not able to
> fix
> > > this error.
> > > Has anyone got an idea ?
> >
> > check that the columns in your pdb file are correct.
> > search for q2 in your pdb file.
> >
> > > Thanks a lot and have a nice day using gromacs
> > > greeting
> > > joern
> > > _______________________________________________
> > > 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.
> > > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > --
> > David.
> >
> ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> >
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Mon, 6 Nov 2006 15:37:42 +0200
> > From: Alexei Krukau
> <alex at heineken.chemie.uni-dortmund.de>
> > Subject: [gmx-users] Smooth surface
> > To: gmx-users at gromacs.org
> > Message-ID:
> <200611061437.42349.alex at heineken.chemie.uni-dortmund.de>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Dear Gromacs users,
> > I would like to ask, if there is a possibility to create a smooth
> > (unstructured) hydrophobic or hydrophilic wall in Gromacs?
> > --
> > Alex Krukau
> > Physical Chemistry II a
> > University of Dortmund
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Mon, 6 Nov 2006 15:15:56 +0100
> > From: Joern Lenz <JLenz at zbh.uni-hamburg.de>
> > Subject: Re: [gmx-users] Atom q2 not found in rtp database in residue
> > TRP
> > To: gmx-users at gromacs.org
> > Message-ID: <200611061515.56099.JLenz at zbh.uni-hamburg.de>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > >>Joern Lenz wrote:
> >
> > >>dear gromacs users,
> >
> >
> > >>i am performing a simulation of a system of a protein together with a
> DNA
> > >>using the amber03 forcefield which i loaded down from
> > >>http://folding.stanford.edu/AMBER.html. I converted all
> LYS residues in my
> > >>pdb file into LYP and all HIS into HIP (please correct me if you think
> that
> > >>this does not make sense). Does anyone know a script or program which
> > >>automatically converts pdb files into amber pdb files so that i can use
> the
> > >>amber03 FF without changing atoms here and there ?
> > >>
> > >>
> > >>QUESTION: When i start pdb2gmx there always occurs the same error:
> > >>"Atom q2 not found in rtp database in residue TRP"
> > >>
> > >>I cannot recognize where this error comes from and so i am not able to
> fix
> > >>this error. Has anyone got an idea ?
> >
> > >check that the columns in your pdb file are correct.
> > >search for q2 in your pdb file.
> >
> > I checked both suggestions but the error is still there.
> > what can i further do to run pdb2gmx correctly ?
> > thnaks a lot for ideas.
> > Joern
> >
> > >>Thanks a lot and have a nice day using gromacs
> > >>
> > >>greetings joern
> > >>_______________________________________________
> > >>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 [EMAIL PROTECTED]
> > >>Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> >
> >
> >
> > >--
> > >David.
> >
> >________________________________________________________________________
> > >David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > >Dept. of Cell and Molecular Biology, Uppsala University.
> > >Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > >phone: 46 18 471 4205 fax: 46 18 511 755
> > >[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
> >
> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >_______________________________________________
> > >gmx-users mailing list gmx-users at gromacs.org
> > >http://www.gromacs.org/mailman/listinfo/gmx-users
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Mon, 6 Nov 2006 11:14:11 -0500
> > From: Pradip K Biswas <p.biswas at csuohio.edu>
> > Subject: [gmx-users] Re: Fw: gmx-3.3.1_cpmd-3.11.1 with mpirun
> > To: gmx-users at gromacs.org
> > Cc: cseifert at bph.ruhr-uni-bochum.de
> > Message-ID:
> > <
> OFAE661ABB.57DC1FCE-ON8525721E.00593075-8525721E.00593089 at csuohio.edu>
> >
> > Content-Type: text/plain; charset="us-ascii"
> >
> > An HTML attachment was scrubbed...
> > URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20061106/4b409567/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Mon, 6 Nov 2006 10:19:05 -0800
> > From: "David Mobley" <dmobley at gmail.com>
> > Subject: Re: [gmx-users] (dH/dl) calculation
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Message-ID:
> > <
> bc2c99750611061019x38c0fdg24b2c409e81f8c7d at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Mauricio,
> >
> > I'm somewhat confused by your question and notation. However, I think
> > the basic answer is something like this: In molecular dynamics, you
> > know the Hamiltonian from which you are sampling; call it H(x,p, l),
> > where x denotes all of the positions, p the momentums, and l lambda.
> > This, of course, is closely linked to the potential energy. Anyway, at
> > any snapshot, you can simply take the derivative dH(x,p,l)/dl, and you
> > have dH/dl at that snapshot. This is usually straightforward since you
> > know the dependence of all of the terms in your Hamiltonian on lambda,
> > so you actually have the functional form for dH/dl as well -- so it
> > just involves taking the appropriate combination of positions,
> > momentums, etc. This is of course all handled internally by the code.
> > <dH/dl>, then, is just the time-average of dH/dl, which can be
> > evaluated every step by the code.
> >
> > I am not sure if that's helpful at all, as I'm not entirely sure what
> > problem you're having. After all, whenever you do TI calculations in
> > GROMACS, the code gives you back dG/dl (or dH/dl, or dA/dl) for every
> > snapshot in an xvg output file. Are you just confused about how the
> > code gets this (I think I just answered that above), or are you trying
> > to figure out how to use it? If you're confused about how to use it,
> > try to ask a question that relates to the specific issue you're
> > confused about.
> >
> > Best wishes,
> > David Mobley
> > UCSF
> >
> >
> > On 11/5/06, Mauricio Sica <msica at unq.edu.ar > wrote:
> > > Dear experts
> > >
> > > I am doing FEP (thermodynamic integration method) simulations.
> > > I have a questions about <dH/dl> calculation in GROMACS.
> > > Take in mind equation 3.77 from the GROMACS 3.3 manual.
> > > There, dA/dl is calculated as
> > >
> > > dA/dl = SS{ (dH/dl) exp()dp dq } / SS{ exp()dp dq = <dA/dl>NVT;l }
> > >
> > > where SS are doble integrals (sorry for the notation).
> > >
> > > My question is: how is (dH/dl) (in the middel-term of the equation)
> > > calculated?
> > > My idea is that the difference V(L=1)-V(L=0) is calculated for every
> time
> > > step (irrespective of the lambda value of the simulation) and <dG/dl> is
> > > the time average of that difference.
> > >
> > > <dG/dl> = < V(L=1)(i)-V(L=0)(i)/1 >
> > >
> > > Is this correct?
> > >
> > >
> > > Thanks
> > >
> > >
> > >
> > > _______________________________________________
> > > 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.
> > > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> > >
> >
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Mon, 6 Nov 2006 16:37:58 -0600
> > From: "Mohan Boggara" < mohanbabu.boggara at gmail.com>
> > Subject: [gmx-users] Molecular volume
> > To: gmx-users at gromacs.org
> > Message-ID:
> > <
> 2fdedacb0611061437u4dac16as1a6879b9c37f7247 at mail.gmail.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Dear users,
> > Is there a way to calculate molecular volume of small solutes that we use
> in
> > simulations?
> >
> > Mohan
> >
> > --
> > Mohan Boggara
> > Graduate Research Assistant
> > Dept of Chemical Engineering
> > University of Houston
> > S222 Engg Bldg 1, 4800 Calhoun Rd,
> > Houston, Texas-77204, USA
> > Mobile: 1-832-643-5729
> > Office: 1-713-743-4314
> > http://polymer.chee.uh.edu/
> >
> > Knowledge is power--unknown
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20061106/13f32735/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 8
> > Date: Mon, 6 Nov 2006 14:58:34 -0800
> > From: "David Mobley" <dmobley at gmail.com>
> > Subject: Re: [gmx-users] Molecular volume
> > To: "Discussion list for GROMACS users" < gmx-users at gromacs.org>
> > Message-ID:
> >
> <bc2c99750611061458w2eaaf7c0p866dc6c6d19a550 at mail.gmail.com
> >
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> > I think in 3.3, there was a new option added to g_sas that allows you
> > to calculate the solvent accessible volume, which may be what you
> > want. Try searching the list.
> >
> > David
> >
> >
> > On 11/6/06, Mohan Boggara <mohanbabu.boggara at gmail.com> wrote:
> > > Dear users,
> > > Is there a way to calculate molecular volume of small solutes that we
> use in
> > > simulations?
> > >
> > > Mohan
> > >
> > > --
> > > Mohan Boggara
> > > Graduate Research Assistant
> > > Dept of Chemical Engineering
> > > University of Houston
> > > S222 Engg Bldg 1, 4800 Calhoun Rd,
> > > Houston, Texas-77204, USA
> > > Mobile: 1-832-643-5729
> > > Office: 1-713-743-4314
> > > http://polymer.chee.uh.edu/
> > >
> > > Knowledge is power--unknown
> > > _______________________________________________
> > > 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.
> > > 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
> >
> >
> > End of gmx-users Digest, Vol 31, Issue 19
> > *****************************************
> >
>
>
>
> --
>
> Mohan Boggara
> Graduate Research Assistant
> Dept of Chemical Engineering
> University of Houston
> S222 Engg Bldg 1, 4800 Calhoun Rd,
> Houston, Texas-77204, USA
> Mobile: 1-832-643-5729
> Office: 1-713-743-4314
> http://polymer.chee.uh.edu/
>
> Knowledge is power--unknown
> _______________________________________________
> 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.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
More information about the gromacs.org_gmx-users
mailing list