Hi all,
I am trying to compute the order parameters for the sn1 and sn2 chains of
DOPC (CHARMM36) in bilayer . I am using the g_order tool (v4.6.3).
I have constructed for each DOPC chain two index files that contains in
the first one all the Carbon atoms where the first Carbon is C=O and the
las
93.50 110.06 P 1
Did I miss something important here about PR and crystals?
SA
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n chain backbone. Again how to do that ?
Your guidance would be helpful for me.
Best
SA
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Hi all,
:
A quick question here:
Does the g_msd program (v4.5.5) take into account the finite size
effect due to PBC when it computes/gives translational diffusion ?
sa
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>
> Thank you Olivier for your response.
>
SA
> --
>
> Message: 2
> Date: Thu, 28 Jul 2011 11:20:44 +0100
> From: Oliver Grant
> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
> To: Discussion list f
>
> Yeah I have also found this page. Finally I did the conversion. I am
> currently testing the parameters.
>
Thank you Austin and Mark for your help
SA-
>
> --
>
> Message: 4
> Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT)
> From: &qu
that in the AMBER ff port in GROMACS, the
multiplicity values are always set to > 0 and the barrier heights have
sometime a negative value.
Thank you again for your advice.
SA-
Message: 1
> Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT)
> From: "Austin B. Yongye"
> S
0.0-3. Dimethyl
phosphate
1 -0.50 0.0-2.
10.10 0.0 1
Thank you in advance, for your help
SA
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Ok Thank you Justin for this clarification
>
>
>
> sa wrote:
> > Dear All,
> >
> > I have simulated 6 peptides (with 7 AA each capped in N and C termini)
> > in water and trehalose. During all the simulation time, the six peptides
> > have b-sheet con
5
# Totals60246010
# SS %0.64 0.26 0.64 0.11
I can understand how the %SS values are obtained in the example given in
http://redmine.gromacs.org/issues/683, but not in my case. Could you tell me
how the %SS is obtained the output above.
Thank you in advance for your help
SA
-
Thank you David
A bientôt
SA
> --
>
> Message: 1
> Date: Sun, 10 Apr 2011 11:17:15 +0200
> From: David van der Spoel
> Subject: Re: [gmx-users] Different g_sas values between AMBER, CHARMM
>and
the carbon atoms
(including the headgroup carbon atoms).
Thank you
SA
>
> On 2011-04-09 19.06, sa wrote:
> > Dear All,
> >
> > I have simulated three DPC micelles with the same size (54 lipids) with
> > different force fields (CHARMM, AMBER et GROMOS53A6) and computed
from the correct mass and radius of the atom type.
WARNING: could not find a Van der Waals radius for 54 atoms
It is important ?
Thank you in advance for your advices.
SA
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Dear All,
Finally, I resolved my problem by contacting the author of the paper (thanks
to D. Poger). They gave me the correct value for the epsilon and sigma
(0.2137 nm instead of 0.3137 nm in the paper).
SA
>
>
> Message: 2
> Date: Tue, 29 Mar 2011 09:45:34 +1100
> Fro
atom
with itself, correct ? And the nonbond_types section, the comb-rules with
the other atoms types.
So if I take into account only the OM atom, as an example, why I obtained
different values for C6 and C12 terms in the [ atomtypes ] section.
Thank you again for your
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
> - next part --
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users
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.
OM8 0.000 0.000 A 0.0022619536 7.4149321e-07
So your advices are welcome.
SA
2011/3/28 sa
> Thank
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,
> >
> &
help.
SA
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OK Angel,
I will contact you off-list
SA
>
> 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.
&g
Ok Justin,
So which gmx tool i can use to obtain the angle between two vectors defined
by two atom pairs ?
SA
sa wrote:
> > Hi all
> >
> > This message is related with my previous message (see below) about the
> > calculation of the order value for the DPC alkyl chain i
rrors
---
Did I make a error, what is the correct approach. to obtain the angle
between 2 vectors ?
Thank you in advance
SA
> --
>
> Message: 3
> Date: Wed, 16 Mar 2011 10:06:44 +0100
> From: ?ngel Pi?eiro
Thank you Angel, I will try your suggestion.
Cheers
SA
>
>
>
> 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 paramet
Dear all,
I would like to compute the order parameter tensor elements of a DPC micelle
with respect to a vector direction (for example the vector from the
center of mass of the micelle to the phosphorus atom). It is possible with
g_order (4.5.3). if yes how ?
Thank you in advance.
--
gmx-users m
OK, i will try your suggestion.
Thank you
SA
sa wrote:
> > Yes justin, the average is not 0 but around 0° (0.584577). But how to
> > obtain the Average normalized dihedral distribution for example
> > this dihedral? is few words the figure with g_angle ?
> >
>
Yes justin, the average is not 0 but around 0° (0.584577). But how to obtain
the Average normalized dihedral distribution for example this
dihedral? is few words the figure with g_angle ?
http://cmt.dur.ac.uk/sjc/thesis_dlc/node106.html
Thank you again
> sa wrote:
> > Dear
the
middle of the alkyl chain, i obtain an average value 0° (!!) and the
following figure
http://www.hostingpics.net/viewer.php?id=825755angdist.png
This is not what i expect How to obtain simply the classical normalized
function from g_angle ?
Thank you in advance for your advices
SA
--
0.9 g/cm3. Did i compute the expected function
with above command ? If not, how to obtain the rdf (in g/cm3) for each
components ?
Thanks for the help.
SA
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16.4 ).
What is wrong with command used above. Did i forget something ?
Thank you in advance for your help.
SA
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the accessible surface area with respect to solvent
for some residues of the peptide and especially for the single TRP of the
peptide (TRP553) and compare with the SA obtained for the same peptide in
water. By examining several configurations of the peptide in the B system
at the end of the
ted in the mailing list few days ago,
unfortunately no response was given:
http://www.mail-archive.com/gmx-users@gromacs.org/msg35963.html
Thanks in advance
SA
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h
version and finally how the charge group
distribution to compute the force during the simulations.
http://hpics.li/9ed5ee1 --> Secondary structure vs. time
http://hpics.li/7cf1625 --> RMSD vs. time
So i suspect that the errors come from the use a bad version of the CHARMM27
ff
Thank you all for
ere there are more terms). =-O To be sure that this difference
has no impact in the MD, i going to do other MD.
I will come back soon. Thanks you again
SA
>
> Cheers
>
> Tom
>
> On 25/11/10 22:42, sa wrote:
> > Dear All,
> >
> > In a previous message
&g
-463287 24955.755 -165.768
(kJ/mol)
I am particularly eager to obtain from you some comments and advices about
these findings. Thanks you so much for your help.
SA
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Ple
that chargegrp "yes" option
should not be used in MD with CHARMM force field in GROMACS, as it was
discussed recently in this mailing list (for example
http://lists.gromacs.org/pipermail/gmx-users/2010-September/054106.html).
SA
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>
>
> sa wrote:
> >
> > On 13/11/2010 4:07 AM, sa wrote:
> > > Dear All,
> > >
> > > I would like to compute the average 2D density distribution of the
> > > water around 6 peptides aggregated in the cluster with
> On 13/11/2010 4:07 AM, sa wrote:
> > Dear All,
> >
> > I would like to compute the average 2D density distribution of the
> > water around 6 peptides aggregated in the cluster within the
> > simulation box with gromacs, for that I think that g_densmap
Dear All,
I would like to compute the average 2D density distribution of the water
around 6 peptides aggregated in the cluster within the simulation box with
gromacs, for that I think that g_densmap is the the good tool (correct ?).
However it is not very clear for how to use g_densmap. Below the
r your help.
sa
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