[gmx-users] Re: gmx-users Digest, Vol 83, Issue 196
sa
sagmx.mail at gmail.com
Mon Mar 28 14:27:18 CEST 2011
Thank you Justin,
It is good to know i am not alone to not understand. So I will ask to the
authors the reason of this discrepancy.
Bye
SA
2011/3/28 <gmx-users-request at gromacs.org>
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> Message: 3
> Date: Mon, 28 Mar 2011 07:27:11 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] mathematical expression to obtain the C6 and
> C12 LJ terms for the GROMOSXX ff family
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D90708F.7000003 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> sa wrote:
> > Thank you Justin for your response
> >
> >
> > I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137
> > and epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol
> > 31, 6, 1117) as an example. Unfortunately i can't retrieve the C6 and
> > C12 values given for the same in the GROMOS53A6 ffnonbonded.itp. I used
> > the following command
> >
>
> I cannot explain this discrepancy. Going back to the actual 53A6 source
> (Oostenbrink et al. JCC 2004: 25: 1656-1676), the parameters in
> ffnonbonded.itp
> are correct with respect to the original force field. The fact that Poger
> et
> al. claim the parameters are the same does not make sense to me. You may
> wish
> to contact the authors of that paper directly if you have questions about
> reproducing their results. I also find it curious that they list their
> values
> in sigma/epsilon rather than the conventional C6/C12 used by Gromos96 force
> fields.
>
> -Justin
>
> > g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output
> >
> > c6 = 4.66239e-03, c12 = 4.44320e-06
> > sigma = 0.31370, epsilon = 1.22310
> > Van der Waals minimum at 0.352116, V = -1.2231
> >
> > Fit of Lennard Jones (12-6) to Buckingham:
> > A = 199065, B = 34.0796, C = 0.00466239
> >
> > Back Off! I just backed up potje.xvg to ./#potje.xvg.8#
> >
> > gcq#342: "Ich war schwanger, mir gings zum kotzen" (Nina Hagen)
> >
> >
> > Did I miss something ?
> >
> > Thank you again for your help
> >
> > SA
> >
> >
> >
> >
> > sa wrote:
> > > Dear All,
> > >
> > > I would like to compute the C6 and C12 LJ terms for the GROMOS
> > 53A6 ff
> > > for a new atom type and incorporate them in my ffnonbonded.itp.
> Does
> > > anybody know the mathematical expressions used to obtain these
> terms
> > > from a sigma (nm) and an epsilon (kj/mol) values manually.
> > >
> >
> > g_sigeps can do this for you. Otherwise, you can convert between
> > the two common
> > forms of the Lennard-Jones equation.
> >
> > -Justin
> >
> > > Thank you for your help.
> > >
> > > SA
> > >
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> >
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 28 Mar 2011 14:07:31 +0200
> From: sa <sagmx.mail at gmail.com>
> Subject: [gmx-users] Re: mathematical expression to obtain the C6 and
> C12 LJ terms for the GROMOSXX ff family
> To: gmx-users at gromacs.org
> Message-ID:
> <AANLkTimWtTB4V_=NgPBVP9GA4zRnAroxNH-rQT-PrE5Y at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Sorry I forget to say in my previous mail that the values obtained by
> g_sigeps_mpi are not similar to the values given in
> the GROMOS53A6 ffnonbonded.itp for the OM atom.
>
> OM 8 0.000 0.000 A 0.0022619536 7.4149321e-07
>
> So your advices are welcome.
>
> SA
>
>
> 2011/3/28 sa <sagmx.mail at gmail.com>
>
> > Thank you Justin for your response
> >>
> >
> > I have tried g_sigeps with the OM type LJ values (sigma (nm) = 0.3137 and
> > epsilon (kj/mol) = 1.2231 given in Poger et al. Paper (JCC Vol 31,
> 6,
> > 1117) as an example. Unfortunately i can't retrieve the C6 and C12
> values
> > given for the same in the GROMOS53A6 ffnonbonded.itp. I used the
> following
> > command
> >
> > g_sigeps_mpi -sig 0.3137 -eps 1.2231 and obtained the output
> >
> > c6 = 4.66239e-03, c12 = 4.44320e-06
> > sigma = 0.31370, epsilon = 1.22310
> > Van der Waals minimum at 0.352116, V = -1.2231
> >
> > Fit of Lennard Jones (12-6) to Buckingham:
> > A = 199065, B = 34.0796, C = 0.00466239
> >
> > Back Off! I just backed up potje.xvg to ./#potje.xvg.8#
> >
> > gcq#342: "Ich war schwanger, mir gings zum kotzen" (Nina Hagen)
> >
> >
> > Did I miss something ?
> >
> > Thank you again for your help
> >
> > SA
> >
> >
> >
> >
> >> sa wrote:
> >> > Dear All,
> >> >
> >> > I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff
> >> > for a new atom type and incorporate them in my ffnonbonded.itp. Does
> >> > anybody know the mathematical expressions used to obtain these terms
> >> > from a sigma (nm) and an epsilon (kj/mol) values manually.
> >> >
> >>
> >> g_sigeps can do this for you. Otherwise, you can convert between the
> two
> >> common
> >> forms of the Lennard-Jones equation.
> >>
> >> -Justin
> >>
> >> > Thank you for your help.
> >> >
> >> > SA
> >> >
> >>
> >> --
> >> ========================================
> >>
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> MILES-IGERT Trainee
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >> ========================================
> >>
> >>
> >>
> >
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> Message: 5
> Date: Mon, 28 Mar 2011 12:37:51 +0100
> From: Andr? Ferreira <aff at eq.uc.pt>
> Subject: [gmx-users] No DD grid found
> To: gmx-users at gromacs.org
> Message-ID: <4D90730F.7060301 at eq.uc.pt>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear all,
>
> I am having some problems with some molecules that I am currently
> simulating. I got simulation box that is constituted by 100 oligomer
> molecules (190 atoms each), in a cubic box with 7 nm side (50K). Since
> the molecule is quite long I am using a rcoulomb of 2.8 nm and rvdw of
> 3.4 nm. When I try to perform the simulation mdrun can't find DD grid
> for more than 48 cores, which is a huge handicap. This is the first time
> that I am working with longer molecules, and I never had this problem.
>
> Really appreciate the help,
> André
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 28 Mar 2011 23:13:04 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] converting L to D amino acid in the CHARMM
> force field in GROMACS where to alter dihedral
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D907B50.1040902 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 28/03/2011 8:45 PM, maria goranovic wrote:
> > That would mean that a new residue type will not be required? I just
> > need the correct input D-coordinates?
>
> Try it, before asking about it :-) I said "I suspect you do not need to
> change anything about the topology", but I haven't actually done
> anything like this ever. Topologies and code shouldn't care about
> chirality, so you shouldn't need to do anything other than input the
> configuration you want.
>
> Mark
>
> > On Sat, Mar 26, 2011 at 2:02 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> > <mailto:Mark.Abraham at anu.edu.au>> wrote:
> >
> > On 26/03/2011 2:27 AM, maria goranovic wrote:
> >> Yes, that would be the correct way to do this. I was hoping to
> >> take a shorter route, and just modifying a couple of dihedrals in
> >> the topology files output by pdb2gmx without having to make a new
> >> residue. Is that not possible at all ?
> >
> > Unlike (say) AMBER's leap, pdb2gmx doesn't generate coordinates in
> > a general sense. It generates a topology that matches given
> > coordinates, fixing a few details as directed. It will fill
> > valences with hydrogen atoms, generate terminal groups, organize
> > disulfides, and choose protonation states of titratable residues,
> > but it won't change geometries in the way you seem to want.
> >
> > Neither does anything in the .top/.itp files stipulate the
> > chirality of any center (in all-atom models). Various dihedral
> > angles change sign with chirality, but the dihedral functions are
> > all symmetric about the y-axis (i.e. even). So I suspect you do
> > not need to change anything about the topology. Just use a
> > molecule builder to change the chirality of the relevant center in
> > the input file to pdb2gmx.
> >
> > Mark
> >
>
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