Hi,
The force you assigned for position restrain may not be enough to hold
the ligand in the proper position. If u follow the gromacs tutorial ...the
simulation method is not wrong.
On Tue 16 Apr, 2019, 11:22 AM RAHUL SURESH Hi Users.
>
> A basic clarification on protein and small molecule in
Hi,
You have to compute all the pairwise interactions if you want to compare
all the pairwise interactions.
But I'm deeply skeptical that you can learn anything from this anyway. The
potential energy of typical force fields is not constructed to be
decomposable, and such an analysis neglects the
Hi,
I don't recall gmx analyze computing standard errors. But gmx analyze -h
will report on what it does do :-) Does that help?
Mark
On Tue, 16 Apr 2019 at 08:58, Raag Saluja wrote:
> Hi!
>
> What percent error is calculated as standard error by gmx analyze? 5%?
>
> Thank you in advance and re
Or another way to keep the protonated state of residue is using -asp, -glu,
-his ... and then you can manually assign the protonation state
On Tue, Apr 16, 2019 at 1:06 AM Justin Lemkul wrote:
>
>
> On 4/15/19 6:30 PM, Neena Susan Eappen wrote:
> > Hello gromacs users,
> >
> > I started with a p
Dear Gmx users,
I've been using Gromacs to perform Principal Component Analysis on my
trajectories.
1- With gmx anaeig, we can plot a 2d projection of a trajectory on eigenvectors
1 and 2 (for example). I would like to know if there is a way to obtain the
same plot but where the points are col
thank so much for your reply. Is there any loop which i can use to
calculate all the residue pair wise interaction energy. So all the data can
be handled.
On Tue, Apr 16, 2019 at 2:29 PM Mark Abraham
wrote:
> Hi,
>
> You have to compute all the pairwise interactions if you want to compare
> all
Hi GROMACS users,
The official release of GROMACS 2019.2 is available!
This second patch release fixes several issues found since the last
patch release of GROMACS 2019. We encourage all users of the 2019
series to update to 2019.2. Please see the link to the release notes below
for more detai
Hello again,
apologies for messing up the subject line, this is of course for the
2019.2 point release!
Cheers
Paul
On 16/04/2019 13:41, Paul bauer wrote:
Hi GROMACS users,
The official release of GROMACS 2019.2 is available!
This second patch release fixes several issues found since the
On Tue, Apr 16, 2019 at 1:57 PM Bratin Kumar Das <
177cy500.bra...@nitk.edu.in> wrote:
> Hi,
> The force you assigned for position restrain may not be enough to hold
> the ligand in the proper position. If u follow the gromacs tutorial ...the
> simulation method is not wrong.
>
Thank you. I a
Hi,
I met some errors when running make check after compiling the Gromacs 2019.
Really appreciate it if anyone could help me.
The Cmake info is listed as below:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DGMX_SIMD=AVX2_256
-DCMAKE_INSTALL_PREFIX=/home/sly1993/sly1993/soft
Hi
Use higher force constant and see what is happening
On Tue 16 Apr, 2019, 6:14 PM RAHUL SURESH On Tue, Apr 16, 2019 at 1:57 PM Bratin Kumar Das <
> 177cy500.bra...@nitk.edu.in> wrote:
>
> > Hi,
> > The force you assigned for position restrain may not be enough to
> hold
> > the ligand i
Dear Gromacs users,
I want to simulate a protein embedded in a membrane made of POPC
phospholipid.
I have some experience with MD, but it is the first time that I am
simulating a membrane protein.
I am following the tutorial of KALP15 in DPPC membrane
(http://www.mdtutorials.com/gmx/membra
Hi Emilio,
> Is there a way of doing it using gromacs tools?
Perhaps you can use gmx genconf?
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-genconf.html
Have a look and see if it would work for you. I'm sure there are other
ways that may be better, but this is the first that comes
Sorry for the double post, but you could also try using CHARMM-GUI.
http://www.charmm-gui.org/
That way you don't have to deal with implementing the Berger lipids into
the gromos force field (note that CHARMM is all-atom while gromos is
united-atom). I have only used it to make a pure lipid bilay
I am using OPLS-AA force field and there are no parameters for protonated
carbonyl for alanine residue. How do I go about this?
Thank you,
Neena
From: Neena Susan Eappen
Sent: Monday, April 15, 2019 10:30 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject:
On 4/16/19 3:21 PM, Neena Susan Eappen wrote:
I am using OPLS-AA force field and there are no parameters for protonated
carbonyl for alanine residue. How do I go about this?
What exactly are you trying to protonate? The oxygen in a peptide bond
is not protonated. The C-terminus can be neut
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Hi all,
I'm currently trying to analyze the energy balance of a trajectory
where I see various kinds of spatial partitioning of my molecules. I'd
like to be able see a breakdown based on spatial group and atom type.
However, I only know which molecules end up in which spatial region
after
​Dear all
How can I translate the OPLS parameters to Ryckaert-Bellemans parameters
(C0,C1,C2,C3,...) when the phase angles (f1,f2,f3,f4) are not zero.
V=V0/2+V1/2(1-cos(Q-f1))+V2/2(1-cos(Q-f2))+V3/2(1-cos(Q-f3))+V4/2(1-cos(Q-f4))
Many thanks
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Hi all,
I am building the 2019.2 version, latest CUDA libs (older 2018 version
works fine). While building, I am getting a ton of warnings as shown below,
while the build does not terminate. Is this okay, or do we need to do
anything at this point?
Thanks,
Alex
localstuff/src/gromacs/mdlib/nbn
Okay, more interesting things are happening.
At the end of 'make' I get a bunch of things like
.. nbnxn_cuda.cu(373): warning: variable "dim_grid" was
declared but never referenced
-bash: syntax error near unexpected token `373'
More errors during 'make check' right after " Buildi
Dear Gromacs users,
I am trying to simulate an "infinite" protein chain by covalently bonding
the last residue of my structure to the first residue across the periodic
boundary. I have modified the topology file to include these bonded
interactions and have specified "periodic-molecules=yes" in my
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