You didn't give us much info about your system, so I will assume that your
box is a rectangular prism and that all the cylinders are necessarily
oriented along the z axis (e.g., because they are "infinite"/periodic).
Since the center of mass (COM) of each cylinder must be a point on its
axis,
Dear all,
There is an inconsistency in the truncated octahedron entry in table 3.1
of the reference manual (version 2018 and all previous ones I checked).
The value indicated for the bc and ab angles is 71.53 degrees, but the
vectors a, b and c indicated in the table give the value 70.53
Hi Vidya,
You should try to make your model "fit" into the existing forcefield you
will be using. Also, you should validate the model with known physical
properties (e.g., density, self-diffusion, shear viscosity, isothermal
compressibility). It's usually difficult to get them all good, of
?
Nidhi
On 30 May 2017 8:55 p.m., "Antonio Baptista" <bapti...@itqb.unl.pt> wrote:
Hi Nidhi,
If I remember correctly (and your use of "p2" suggests so), that should be
the ensemble average of the 2nd-order Legendre polynomial of the angle
between the molecular axis and
Hi Nidhi,
If I remember correctly (and your use of "p2" suggests so), that should be
the ensemble average of the 2nd-order Legendre polynomial of the angle
between the molecular axis and the membrane normal, right?
Although the order parameter computed by "gmx order" uses that same
Hi Mohsen,
I suggest you have a look at the QRB 1977 review by Seelig, that Tom
already mentioned. Like for the planar case, they discuss how spectra of
cylindrical lipid phases are related to the order parameter tensor (but I
never looked into the details for that case). Anyway, I don't know
Hi João,
I used gangle to compute several angle distributions relative to the
z-axis membrane normal, but that was almost a year ago, so I don't recall
the details. But I can tell you that, after many failed attempts, I gave
up from using fancy stuff in the -group1 and -group2 options.
Hi Billy,
I know that people from the University of Minho, Portugal, have
parameterized several non-proteinogenic amino acids for GROMOS 54A7,
making the parameters freely available. At least two papers are published:
http://dx.doi.org/10.1021/jp4074587
http://dx.doi.org/10.1021/jp505400q
On Wed, 8 Jun 2016, Tsjerk Wassenaar wrote:
Hey :)
That usually gives a fitted ensemble that more closely retains the
original RMSD values between all pairs of structures.
This should read: ... a fitted ensemble of which the sum of the traces of
all pairwise inner product matrices is
Hi James,
If your molecule shows some flexiblility, I would suggest using as a
reference the structure of your original ensemble that produces the fitted
ensemble with the lowest sum of RMSD values to that structure (or their
square). That usually gives a fitted ensemble that more closely
On Fri, 8 Jan 2016, Bin Liu wrote:
Hi Tsjerk,
I replicated their settings in their papers. The system size I used is
larger than what they had. Could you elaborate on the reference used for
fitting? Thank you so much.
About the importance of the reference structure used for fitting in
On Wed, 5 Aug 2015, Justin Lemkul wrote:
On 8/5/15 10:32 AM, Smith, Micholas D. wrote:
OPLS-AA 2001 (the one implimented in gromacs) can be a little slow in
folding
(in both my experience, and from doi:10.1016/j.bpj.2009.04.061 ). That is
not necessarily a bad thing if the peptide is
Tsjerk, that's one of the coolest explanations of PCA I've ever read! :)
Just one additional comment for Brett: Tsjerk's example assumes implicitly
that your hands are actually moving parallel to the desk on average. On my
desk, the meal is usually on top of the pile of papers that
Hi James,
Yes, but all you need are the 1D projections, since they are the
coordinates in the PCA reference frame. So, just combine them in any way
you want, as Tsjerk indicated. Also, keep in mind that there is actually
no transformation of the conformation space when you do PCA, just a
Hi,
Our PB/MC/MD approach to constant-pH simulations is implemented up to
version 4.0.7 of GROMACS, but we don't currently have a usable
distribution -- after using some collaborators as guinea pigs, we came to
the conclusion that the current implementation is unintelligible, since no
one
On Thu, 6 Nov 2014, Téletchéa Stéphane wrote:
Le 06/11/2014 06:16, Antonio Baptista a écrit :
In particular, the virial-based instantaneous pressure (call it P')
computed in simulations has its ensemble average equal to the thermodynamic
pressure P (check any good book on molecular
Well, it is definitely *not* totally irrelevant to talk about pressure
when doing simulations in the NVT (canonical) or NVE (microcanonical)
ensembles. Pressure, like temperature, volume, energy, numbers of
particles, etc, is a thermodynamic property which is *always* defined for
*any* system
Then, run true NVE, for the reasons we already pointed.
On Sat, 11 Oct 2014, Johnny Lu wrote:
For dynamics with correct rate and correct fluctuation.
On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:
what is it needed for?
Dr. Vitaly V. Chaban
Виталий
Hi Nicola,
On Thu, 11 Sep 2014, nicola staffolani wrote:
Dear GMX community,
regarding the program g_principal and acknowledged the bug reported here
http://permalink.gmane.org/gmane.science.biology.gromacs.user/66719
, I would like to understand what the meaning of the output of this
Well, the terminology is an old one, but not very common. An isometric
ensemble is generally one in which the extension in the mechanical work
term is kept constant. Thus, it may mean that the volume is kept constant
in a volume/pressure system, that the area is kept constant in a
area/surface
On Fri, 7 Feb 2014, Justin Lemkul wrote:
On 2/7/14, 6:08 PM, Antonio Baptista wrote:
Dear all,
This is a follow-up to an old thread on g_principal, which continues (as of
version 4.6.5) to suffer from what I would call a bug or, at least, a very
bad
and misleading choice of output file
Szilárd already activated it a couple of hours ago (just noticed he
replied to me only). The issue is already submitted also. Thanks anyway.
Best,
Antonio
On Wed, 19 Feb 2014, Mark Abraham wrote:
It shows as active to me...
Mark
On Tue, Feb 18, 2014 at 11:46 PM, Antonio Baptista bapti
Dear all,
This is a follow-up to an old thread on g_principal, which continues
(as of version 4.6.5) to suffer from what I would call a bug or, at
least, a very bad and misleading choice of output file names. This
message is primarily a further warning to users, but I also hope that it
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