[gmx-users] Dihedral Restraints

[Jacek Artur Kozuch]

Dear all,

I am a bit confused about [ dihedral constraints ].

I was planning to contraint a dihedral in a "flat-bottom" way, so that
e.g. angles between 120 and 240 deg are sampled, but above 240 and below
140 are basically "not allowed". In other words, I just want a harmonic
potential, where the point of zero-potential is stretched from a point
Theta_0 to a range of Theta_0 +- delta_Theta.

Dihedral restraints seemed to be what I need, at first glance, but I am
confused about the resulting potential obtained from equation 12 in the
manual:
http://manual.gromacs.org/current/reference-manual/functions/restraints.html#dihedralrestraint

The conditions
- |Theta'| > delta_Theta
- |Theta'| <= delta_Theta
and the "(Theta' - delta_Theta)" in the first condition of eq. 12 will do
it in an asymmetric way, with different behaviour at Theta' = +
delta_Theta or Theta' = - delta_Theta.

Therefore, is equation 12 just written in a strange way and it creates a
symmetric flat-bottomed potential or will it really result in such an
asymmetry?

Thanks already for your help.

Best wishes,
Jacek


Dr. Jacek Kozuch

Freie Universität Berlin
Fachbereich Physik
Arnimallee 14
Raum 1.1.35
14 195 Berlin



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[gmx-users] Double-well potential for bonded interaction

[Jacek Artur Kozuch]

Hi,

Does anybody know how to define for a specific bond a double-well potential?

I've looking into the definitions in the gromacs manual
(manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html
and
manual.gromacs.org/current/reference-manual/functions/bonded-interactions.html),
but for now I can only imagine using bond restraints in a similar manner
shown here for position restraints:
manual.gromacs.org/current/reference-manual/functions/restraints.html

It feels like there should be a more elegant way of doing that.

Thanks for your suggestions in advance!

Best,
Jacek


Dr. Jacek Kozuch

Freie Universität Berlin
Fachbereich Physik
Arnimallee 14
Raum 1.1.35
14 195 Berlin


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[gmx-users] Anharmonic/Morse flexible water

[Jacek Artur Kozuch]

Hi all,

I am currently trying out various water models for some solute/solvent
systems and I was wondering if there are any (reliable) anharmonic/Morse
flexbile water models that can be used in Gromacs?

I've seen that can set [ Morse ] for bonds, but don't want to start doing
random changes to available models.

Thanks in advance and stay healthy!

Best,
Jacek

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[gmx-users] itp file for TIP7P

[Jacek Artur Kozuch]

Dear all,

I've seen the recent publication about the tip7p model
(https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03149) and wanted to try it
out in some simple MD simulations.

Since I am still a pretty new Gromacs user, I didn't want to build the itp
file myself and, potentially or most probably, mess up something. Is there
a common github-like depository that I am missing where I could find the
tip7p-parameters.

If not, would be someone willing to help me in putting the itp file
together - the authors haven't responded yet.

Thanks in advance!

Best wishes,
Jacek

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[gmx-users] GROMACS - tip7p itp and gro files - couldn't find them anywhere

[Jacek Artur Kozuch]

Hi all,

I've seen that recent tip7p water model 
(https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03149) and wanted to try it out. 
However, I couldn't find or I missed where the itp and gro files are deposited.

Anybody knows where to find them?

Thanks a lot in advance!

Best,
Jacek
[https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/jpcbfk/2019/jpcbfk.2019.123.issue-21/acs.jpcb.9b03149/20190523/images/large/jp-2019-03149k_0011.jpeg]
Seven-Site Effective Pair Potential for Simulating Liquid Water | The Journal 
of Physical Chemistry B
Constant pressure simulations were carried out to construct a new rigid 
nonpolarizable seven-site water model (TIP7P), which is an effective and 
efficient version of flexible seven-fluctuating-charge water model. In this 
model, the positive charges are located on three nuclei and the negative 
charges disperse on two bond sites at the geometric center of each OH bond and 
two lone-pair sites ...
pubs.acs.org




Dr. Jacek Kozuch
Postdoctoral Researcher - Boxer Lab

Stanford University
Department of Chemistry
Keck Science Building
380 Roth Way
Stanford, California 94305-5012
phone +1 (650) 723-0386
https://web.stanford.edu/group/boxer/


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[gmx-users] Average structure from trajectory

[Jacek Artur Kozuch]

Dear Gromacs Users,

I am trying to obtain an average structure in addition to the rmsf from my 
trajectories.

I tried doing that using 'gmx rmsf', but I was not successful yet.

Thanks in advance for all suggestions!

Best,
Jacek



Dr. Jacek Kozuch
Postdoctoral Researcher - Boxer Lab

Stanford University
Department of Chemistry
Keck Science Building
380 Roth Way
Stanford, California 94305-5012
phone +1 (650) 723-0386
https://web.stanford.edu/group/boxer/


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