Hi
when calculating an energy contribution using g_energy, the units
specified in the plots, as well as in the output tables, are kJ/mol.
This happens even when the -nmol flag is missing (so nmol=1). On the
other hand, the energy units in gromacs are kJ/mol. So I guess that when
a term (a dihedral
I guess there are better solutions but an alternative is to map your
bilayer to MARTINI (http://md.chem.rug.nl/cgmartini/) and then to use
SUGAR-PIE (http://smmb.usc.es/sugarpie/sugarpie.php) to go to from
MARTINI to all-atom CHARMM36.
Hope it helps,
Ángel.
On Tue, 2012-05-01 at 17:25 +0530, An
our web site for more information as well as
to test SUGAR-PIE at http://smmb.usc.es/sugarpie/sugarpie.php
Yours sincerely,
Ángel Piñeiro.
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Dear SA
To be honest I am not sure this can be done by using g_angle, I used my
own code for this calculation. I could send it to you if you send me a
message off the list... but I would prefer to talk with a non-anonymous.
Cheers,
Ángel.
On Wed, 2011-03-16 at 15:58 +0100, sa wrote:
> Hi all
Then, please, let us know how it works for your systems. The results for
my systems were exactly as expected. This allows to evaluate the order
of the C-chains regardless their orientation... but I do not know if
there is a better method to do this. I would be happy to know the
opinion of anyone el
Hi
very recently I faced the same problem with a system that gives micelles
of different geometries and, as far as I saw, g_order don't do that.
Then I decided to compute a kind of local order parameters defined as:
S_i=(3 cos(\theta)-1)/2
where theta is the angle between the segments joining th
Hi Marcelo
your initial box is right, (4.72 nm)^3 = 105.15404e-27 m^3
500 hexane molecules = 500/(6.02e23)*86.16e-3 kg
the density of your initial system = 680.200377454 kg m^-3
The pdb file you sent contained two different structures (I just
realized about this) the first one is in a box of the r
Hi Marcelo
your molecules are not in a box, the head of the pdb you sent to me is:
HEADER
TITLE Built with
Packmol
REMARK Packmol generated pdb file
REMARK Home-Page: http://www.ime.unicamp.br/~martinez/packmol
REMARK
ATOM 1 C1 HEX A
Hi Marcelo
It is always good to see what happens to a known molecule before working
with your target with a new methodology. I took a closer look to your
pdb. You do have different hexane conformations. Anyway it is hard to
believe that your initial box was full of hexane... could you check
again y
Hi Marcelo
1.- perfluorohexane is a quite rigid molecule so I wouldn't expect many
different conformations
2.- your simulation box is far away from the equilibrium
3.- you should inform about which force field and simulation conditions
are you using, for instance: was your simulation run at constan
Hi Marcelo
please, take a look here: DOI: 10.1016/j.jcis.2008.10.018
I guess the authors could send you a pdb.
Cheers,
Ángel.
On Mon, 2011-01-10 at 17:59 +, Marcelo Silva wrote:
> Hi everybody,
>
> I was looking for the structure of perfluorohexane to create the pdb
> file to use wit
r et al (JPC, 97,
> 8343-8360), including the case of unsaturated carbons. It should be
> equivalent to the implementation in GROMAS.
>
> In practice, I don't know the best way to do it, but your proposal
> sounds reasonable.
>
> Javier
>
> Ángel Piñeiro esc
Dear all
I wonder which is the best way to determine the deuterium order
parameters of partially unsaturated chains like the oleoyl chain of
POPC, more specifically I wonder if I should use the -unsat flag in
g_order for this case. I checked several papers on unsaturated lipids,
see for instance:
1
cs.org
> > *Subject:* Re: [gmx-users] Re: individual lateral diffusion coefficients
> >
> >
> >
> > Sorry for the misspell...
> >
> > Thanks Justin.
> >
> > Do you *know* the reason behind?
> >
> > I am trying following that protocol a
n with Martini
> quite a lot and convergence is reached after a few
> microseconds and a multitude of exchanges of lipids
> between contacts with the protein and the bulk. You'd
> then have the issue of which lipid to consider in which
> section ... not a trivial choice.
>
sampling, I don't know).
>
> Thanks
>
> Javier
>
>
> El 02/12/10 13:56, Ángel Piñeiro escribió:
>
> > Hi Javier
> > 1.- you are right! the diff_mol.xvg file I reported was from a
> > previous attempt in which I used the whole lipid molecules wi
t; regarding distances to construct the index file or just make your own
> one.
>
> Good luck
>
> Javier
>
> El 02/12/10 12:50, Ángel Piñeiro escribió:
>
> > I want to add that the MSD as a function of time (msd.xvg file)
> > looks completely linear
> >
&
^2/s. If the
differences are so high for a single lipid bilayer I suspect that I will
not observe significant differences as a function of the distance to the
protein in my simulations of the whole system... probably I am doing
something wrong¿?
Thanks for any advice
Ángel Piñeiro.
--
gmx-users
I want to add that the MSD as a function of time (msd.xvg file) looks
completely linear
Greetings,
Ángel Piñeiro.
On Thu, 2010-12-02 at 12:45 +0100, Ángel Piñeiro wrote:
> Dear all,
> I aim to calculate the lateral diffusion coefficients of lipids as a
> function of the distance to a
Dear all,
I have some membrane protein systems running in our cluster using
gmx4.0.4. The minimizations finish with reasonable potential energy
values (of the order of 10^-5 with maximum forces of the order of
10^-3). Then I am trying to run several 1-ns-long equilibration MD
trajectories with prog
Dear all,
I am trying to run some simulations on our institutional cluster using
gmx4.0.3. My systems are membrane proteins in lipid bilayers although
for the error I am getting I do not think this is important (this is
just my impression because a couple of months ago I got something
similar with
Dear Zgzhang,
I am interested in your answer to your own question since I asked basically
the same several months ago, could you explain it better?
Angel.
De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] En
nombre de Zhang Zhigang
Enviado el: jueves, 27 de noviembre de 2008 04:28 a.m.
Para:
Yes, the index is the residue number that you can take from the pdb file and
the numbers for the atom pairs can be taken from the pdb or from the
topology file. I must have a script that do this work from the pdb... if you
are interested I could look for it (tomorrow).
To understand the numbers yo
You do not need so many distance restraints, it is enough to restraint the
distance between the "O" atom of residue "i" and the "H" atom of the residue
"i+4". Once you have the index for those atoms your [distance_restraints]
section will have one of these lines
ai aj 1 i 1 0.0 0.3 0.8 1
Are you working at constant volume? It would be useful to see your mdp file
Angel.
De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] En
nombre de xianghong qi
Enviado el: miércoles, 05 de noviembre de 2008 10:18 p.m.
Para: Discussion list for GROMACS users
Asunto: [gmx-users] Re: density
This is to report some results that I have been recently obtaining with the
G53a6 parameterization of DPPC and also to ask for advice. I have read in
the mailing list that perhaps this parameterization is worse than that of
Tieleman/Berger to reproduce bilayer properties but I didnt think that
dif
DPPC is direct, it is in the rtp file of the ffG53a6 parameterization... but
I do not know about DMPC
-Mensaje original-
De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] En
nombre de Syma Khalid
Enviado el: sábado, 03 de mayo de 2008 06:39 p.m.
Para: Discussion list for GROMACS users
Asunt
A good reference to understand what you are getting is Biochimica et
biophysica acta 1331 (1997) 235-270, from Tieleman, Marrink and
Berendsen.
On Wed, 2008-04-30 at 08:52 +, pragya chohan wrote:
> Dear users
>
> I am calculating order parameters of palmitoyl which has 16 carbons. I
> made
Thank you David,
what you are suggesting is indeed a difference between substrate-protein
and methane-methane that seems more clearly related with the entropic
correction. If I understood well, what you mean is that the space
accessible to a ligand when it is pulled into a protein is restricted by
Thanks a lot Chris and Berk for your answers. I think that there are (at
least) two different and independent corrections that should be
performed to estimate absolute binding energies from the pmf (that is
indeed my aim) -the correction for the reference state that depends on
the concentration of
Sun, 2008-03-30 at 16:19 -0600, Ángel Piñeiro wrote:
> Dear all,
>
>
>
> My question is related to the calculation of absolute binding Gibbs
> energies more than to the use of Gromacs but it is motivated by a
> paragraph of the Gromacs manual version 3.3 (and also on seve
Dear all,
My question is related to the calculation of absolute binding Gibbs energies
more than to the use of Gromacs but it is motivated by a paragraph of the
Gromacs manual version 3.3 (and also on several papers by Gilson, Karplus,
and others), so I hope someone can help me.
We have cal
This reference J. Phys. Chem. B , 112 (2008), 3529 could be helpful.
Angel Piñeiro.
De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] En
nombre de fabracht sdf
Enviado el: domingo, 30 de marzo de 2008 06:49 a.m.
Para: gmx-users@gromacs.org
Asunto: [gmx-users] Help with water decane interf
> the same for Thioflavin-T. It is a fairly big molecules with I think 39
> atoms. Can you tell me how go about (procedure in detail) to get the FF
> from QM calculation?
>
> I must thank you again.
>
> Nihar
>
> Quoting Ángel Piñeiro <[EMAIL PROTECTED]>:
>
&g
Dear Nihar,
if you contact me off the list I could send to you itp files for native
alpha, beta, and gamma cyclodextrins compatible with the gromos forcefield
(the ones we used in "jpcb (2007) 4383" and "jpcb (2007) 12625").
Unfortunately I do not have the thioflavin.
Regards,
Angel Piñeiro.
--
guess this is not trivial, any tip on this?
>
> This should be your last and desperate solution ... but is certainly
> feasible.
>
> Best
> XAvier
>
> >
> > Angel Pineiro.
> >
> >
> > On Wed, 2008-01-30 at 22:26 +1100, Mark Abraham wrote:
>
negligible.
Another alternative is to edit the code to introduce the new function,
but I guess this is not trivial, any tip on this?
Angel Pineiro.
On Wed, 2008-01-30 at 22:26 +1100, Mark Abraham wrote:
> > Ángel Piñeiro wrote:
> >> Dear David
> >> I have taken a look to the ma
Dear David
I have taken a look to the manual (version 3.3) and I haven't found
information about how to tabulate bonded potential functions (it seems
that Ran is right). On the other hand, what do you mean exactly with
adding two dihedrals?
Angel Pineiro.
> > Date: Tue, 29 Jan 2008 19:18:20 +01
Dear David
I have taken a look to the manual (version 3.3) and I haven't found
information about how to tabulate bonded potential functions (it seems
that Ran is right). On the other hand, what do you mean exactly with
adding two dihedrals?
Angel Pineiro.
> Date: Tue, 29 Jan 2008 19:18:20 +0100
Hi all,
anyone knows how to use (in gromacs) a potential of the type:
U_tors(phi_ijkl) = Sum_n 1/2 k_n [1-cos(n phi_ijkl)]
with n going from 1 to 7?
as far as I saw only the Ryckaert-Bellemans with 6 parameters and a
periodic function are implemented in gromacs. Chapter 4 says something
about th
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