towhee-users Mailing List for MCCCS Towhee

On Wed, Sep 12, 2012 at 12:51 PM, Carlos Campana <cam...@gm...> wrote:

> My question relates to the TraPPE-UA parametrization in towhee for
> carboxylic acids. Could you please clarify on the following?
>
> >From looking into the towhee_ff_TraPPE-UA file I find:
>
> 1-4 Coulombic scale factors do not apply to the following dihedral
> angles related to the carboxylic group, right?
>
> O=c(sp2)   Cco=o(sp2) Och(sp3)   Hoacid
> CH3sp3     Cco=o(sp2) Och(sp3)   Hoacid

Correct.  The one-four logical is set to F for both of those torsions.

> However, you do have a 0.5 factor in the 1-4 Coulomb scaling defined
> for the dihedral:
>
> Cwild    CH2sp3   Cco=o(sp2)  Och(sp3)

I agree that is how the parameters are set in the towhee_ff_TraPPE-UA file.

> The original Kamath et al. 2004 paper mentions nothing about this last
> 0.5. Neither the most recent  J. Phys. Chem. B, 2006, 110 (43), pp
> 21938–21943
> where the problem with the cosine square in the dihedral is fully
> disclosed. Perhaps this is obvious to regular TraPPE users, perhaps
> just because the Kamath work was on linear acids where the "Cwild"
> above will have net charge zero and thus the scaling factor plays no
> role).
> Are the observations above correct? Just trying to reconcile the info
> that exists out there.

Your observations about the torsions as implemented into the
towhee_ff_TraPPE-UA file are correct.  Except in cases where it is
clearly stated that there is no one-four coulombic interaction I have
assumed it is scaled by 0.5 as that appears to be the default for the
TraPPE-UA forcefield.

On the implied question of whether TraPPE-UA as implemented in Towhee
provides valuable information about what the "correct" settings are
based upon the published TraPPE-UA papers I cannot give such clear-cut
answers.  While I am on very friendly terms with the principals in the
TraPPE-UA development community, and certainly can speak with
authority about the early work on alkanes, I am not currently a
TraPPE-UA developer so my knowledge of the correct use of some of the
more recent developments there is not complete.  The Siepmann group
provides a web page with many of their parameters at
http://siepmann6.chem.umn.edu/trappe/intro.php

I certainly would welcome any input if people believe I have
improperly implemented TraPPE-UA (or any of the other force fields in
Towhee).

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com

On Wed, Sep 19, 2012 at 8:46 AM, Salomon Turgman Cohen
<stu...@gm...> wrote:

>    Is there a reason you are maintaining both an email list and a forum?

Because I naturally prefer an email list, while SourceForge
automatically includes a forum.  As some users appear to prefer the
forum I am agreeable to answering questions in whatever format they
are presented.

> Seems to be duplicate effort and that it would be better to maintain just
> one of them.

I find that attempting to optimize my process leads to a dark place
where I spend years asking myself why I provide free support for a
code that I freely distribute without a cushy academic job for my
trouble.  Best to just assume I am an eccentric algorithm artist who
answers questions on a whim and prefers to work on whatever seems the
most interesting that day.

In related news, the SourceForge site just went through another
upgrade so the layout of the web pages there has changed a bit, along
with some internal changes to the location of the SVN repository.

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com

Hey Martin,
   Is there a reason you are maintaining both an email list and a forum?
Seems to be duplicate effort and that it would be better to maintain just
one of them.

Just a suggestion.

Salomon

On Thu, Aug 30, 2012 at 10:53 PM, Marcus Martin <
mar...@us...> wrote:

> Towhee Users,
>
> The new bug-fix version 7.0.3 of Towhee is now available.  This
> resolves some problems that were reported when combining Class 2
> forcefields with the single-atom translation move.
>
> I am also working my way through the back-log of Towhee related emails
> and forum posts.
>
> Finally, Useful Bias has closed so that email address will soon cease
> to function.  The one listed in all the Towhee documentation
> (mar...@us...) is still the suggested one for
> Towhee related business.  General questions are best posted to the
> forums or this mailing list as I have a well-earned reputation for
> being a sporadic email responder.
>
> thanks,
>
> Marcus
>
> --
> Marcus G. Martin
> 88 Martinez Road
> Edgewood NM 87015-8222
> land (505) 286 4457
> cell (505) 363 3179
> www.photobirder.com
>
>
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-- 
Salomon Turgman Cohen
Postdoctoral Associate
Cornell University
(919) 341-9650

Towhee Users,

A report (by Marco Lerario) of inconsistent adsorption results
dependent upon the settings of the 'energy bias' option led to the
discovery of an incorrect term for the correction of the 'energy bias'
option in Towhee.  As far as I can tell, this problem dates back to at
least 2007, and possibly earlier.  Any results using the 'energy bias'
option for cbnc_nb_one_generation in a Towhee release version 7.0.3 or
earlier are suspect and should be compared with results from the new
version 7.0.4.

I apologize for the inconvenience this insidious error has caused
anyone doing adsorption studies.

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com

Hello Marcus (and any other member who might be interested in replying),
My question relates to the TraPPE-UA parametrization in towhee for
carboxylic acids. Could you please clarify on the following?

>From looking into the towhee_ff_TraPPE-UA file I find:

1-4 Coulombic scale factors do not apply to the following dihedral
angles related to the carboxylic group, right?

O=c(sp2)   Cco=o(sp2) Och(sp3)   Hoacid
CH3sp3     Cco=o(sp2) Och(sp3)   Hoacid

However, you do have a 0.5 factor in the 1-4 Coulomb scaling defined
for the dihedral:

Cwild    CH2sp3   Cco=o(sp2)  Och(sp3)

The original Kamath et al. 2004 paper mentions nothing about this last
0.5. Neither the most recent  J. Phys. Chem. B, 2006, 110 (43), pp
21938–21943
where the problem with the cosine square in the dihedral is fully
disclosed. Perhaps this is obvious to regular TraPPE users, perhaps
just because the Kamath work was on linear acids where the "Cwild"
above will have net charge zero and thus the scaling factor plays no
role).
Are the observations above correct? Just trying to reconcile the info
that exists out there.
Thanks,
Carlos Campana

On Wed, Mar 14, 2012 at 1:33 AM, pascal boulet
<pas...@un...> wrote:

> we are performing NVT simulations of molecules adsorbed on a surface and
> we would like to test whether the molecules can make clusters on the
> surface or not. For this the keyword pmavb2in seems most appropriate. We
> are not sure about what values we should choose for the pmavb2ct
> "matrix". Say the surface is entity 1 and molecules are entity 2 is it
> relevant to set:
> pmavb2in
> 0. 1.0
> 0.5 1.0
>
> and what is exactely the meaning of this?

If you set the pmavb2in variable to 0.0 or 1.0 then you are setting up
a situation where you will always accept the move you never attempt,
and never accept the move you always attempt.  That is going to be a
big waste of time.

Ideally you would set pmavb2in (Pbias in the original paper) such that

Pbias * Vout * <Nin> <exp(-beta Delta U)> = (1 - Pbias) * Vin * <Nout +1>

Of course, you most likely don't know these values exactly until after
the simulation, but you could make some assumptions like <Nin> = 1,
you know Vin from the radius you set, you can estimate the binding
energy from a quick 2 molecule simulation, and <Nout +1>/Vout is
approximately the vapor number density.

Hmm, I suppose what would really be clever would be to have Towhee
keep track of some of this information from attempted moves and
automatically adjust Pbias to yield the maximum acceptance rate.
Something to think about as a further advance to the algorithm.  I
might also add some safety features and additional manual
documentation to the next version to keep people from setting Pbias to
0.0 or 1.0.

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com

On Tue, Sep 4, 2012 at 11:00 AM, Amir Vahid <Ami...@nd...> wrote:

> I also found that the Gromos paper for DMSO uses the Lorentz-Berthelot mixrule. Is that a specific reason for explicit treatment of the classical mixrule?

The explicit treatment is used because the 1-4 sigma and 1-4 epsilon
terms for Gromos are not easy to generalize as there are certain
exceptions that are treated differently from the usual
Lorentz-Berthelot rules.  Also, some of the regular nonbonded terms
did not use the Lorentz-Berthelot rule.  If you look at the
ffgromos43a1.F file in the Source directory you will find the details
of which terms had special rules instead of the usual mixing (starting
around line 930).

I realize this makes it difficult to mix and match the Gromos43a1 with
other potentials, but my primary goal was to faithfully implement this
potential.  Force fields of this era were rarely designed to be easy
to combine freely with other potentials.

The older force fields are more of an academic or historical interest
these days as if you were going to extend Gromos for use with
additional molecules and functional groups the logical first step
would be to implement one of their newer parameterizations.

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com

On Tue, Sep 4, 2012 at 10:43 AM, Amir Vahid <Ami...@nd...> wrote:

> I am trying to simulate DMSO (dimethyl sulfoxide) and its mixtures with some ionic liquids with the Gromos force field using towhee and cassandra. However, I see in the towhee_ff_Gromos43A1 the classical mixrule is set to explicit. That means that I should expect 4 nonbond coeffs for self and cross terms. However, I see several "Nonbond Coefficient" columns for each "Atom Type Number". Only the first one agrees with Gromos literatures. I wonder if you could inform me how the program uses the other columns?

I am not sure what you mean by "Only the first ones agrees with Gromos
literatures" as I would hope all of the parameters listed agree with
the Gromos 43a1 literature, but I would be happy to address any direct
statements of which sets of nonbonded parameters do not agree with
particular values in the literature.

The format for the explicit combination only lists the nonbonded
parameters for the self-self, and then subsequently, the self-other so
long as the "other" has a higher index number than the self in order
to avoid duplication.

As per usual with a Lennard-Jones potential in Towhee, the 4 numbers
listed for each nonbonded pairing are the
sigma (general)
epsilon (general)
sigma (used only in 1-4 "nonbonded" interactions)
epsilon (used only in 1-4 "nonbonded" interaction)

Gromos43a1 does not use a straight "scaling" of the 1-4 van der Waals
terms and is the reason why the format in Towhee was set to allow
arbitrary values for the 1-4 van der Waals terms.

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com

On Sat, Sep 1, 2012 at 1:48 PM, Amir Vahid <Ami...@nd...> wrote:

> I wonder if you could tell me why the bond pattern for the fluorine (F) atom in towhee_ff_OPLA-aa is mentioned as s not p (e.g. perfluoropentane?)?

The bond pattern is a very simple-minded notion that is currently only
used in Towhee for certain CBMC algorithms that worked fairly well at
the time I developed them, but I now feel have been replaced with more
powerful and more general algorithms.

The 's' is the correct assignment in this scheme for Fluorine because
it makes one bond.  The other assignments are from a basic chemistry
thinking of the bonding pattern of organic atoms.

http://en.wikipedia.org/wiki/Orbital_hybridisation

Marcus

-- 
Marcus G. Martin
88 Martinez Road
Edgewood NM 87015-8222
land (505) 286 4457
cell (505) 363 3179
www.photobirder.com

Dear Marcus,
I also found that the Gromos paper for DMSO uses the Lorentz-Berthelot mixrule. Is that a specific reason for explicit treatment of the classical mixrule?


Dr. Amir Vahid, Ph.D.
Postdoctoral Research Scientist
Notre Dame Computational Molecular Science and Engineering Laboratory (COMSEL)
Department of Chemical and Biomolecular Engineering
University of Notre Dame 
Notre Dame IN 46556
Tel: +1-(574)631-1426

Dear Marcus,
I am trying to simulate DMSO (dimethyl sulfoxide) and its mixtures with some ionic liquids with the Gromos force field using towhee and cassandra. However, I see in the towhee_ff_Gromos43A1 the classical mixrule is set to explicit. That means that I should expect 4 nonbond coeffs for self and cross terms. However, I see several "Nonbond Coefficient" columns for each "Atom Type Number". Only the first one agrees with Gromos literatures. I wonder if you could inform me how the program uses the other columns?

Best,


Dr. Amir Vahid, Ph.D.
Postdoctoral Research Scientist
Notre Dame Computational Molecular Science and Engineering Laboratory (COMSEL)
Department of Chemical and Biomolecular Engineering
University of Notre Dame 
Notre Dame IN 46556
Tel: +1-(574)631-1426

Dear Marcus,
I wonder if you could tell me why the bond pattern for the fluorine (F) atom in towhee_ff_OPLA-aa is mentioned as s not p (e.g. perfluoropentane?)?

Thanks!


Dr. Amir Vahid, Ph.D.
Postdoctoral Research Scientist
Notre Dame Computational Molecular Science and Engineering Laboratory (COMSEL)
Department of Chemical and Biomolecular Engineering
University of Notre Dame 
Notre Dame IN 46556
Tel: +1-(574)631-1426