Dear gmx developers,
I am trying to use Verlet list for MD simulations using MPI parallelization
only with Gromacs 4.6.5. However, I am getting a segfault during the
initialization of my system before any time step is executed. The simulation
runs perfectly when I am either using Group list or
Sorry you are looking for dihedrals I have just sow that, I think gmx
gangle can not do that.
2014-04-14 23:34 GMT+02:00 Josip Lovrić :
> If I understood you correctly, I think you are looking for gmx gangle. It
> is part of 5.0 version. You need to install new version.
> Check hear
> http://www
Hi Justin,
I tunnel-visioned and completely forgot about the mk_angndx tool. I had
written a similar task for use with ptraj. I should have mentioned that I
am working with .dcd's produced from NAMD with AMBER ff12SB forcefield and
parameters, but that's just a matter of getting pdb2gmx to play
If I understood you correctly, I think you are looking for gmx gangle. It
is part of 5.0 version. You need to install new version.
Check hear http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
2014-04-14 23:09 GMT+02:00 sbowerma :
> Hi Justin,
>
> Thanks for your response. I did
On 4/14/14, 5:09 PM, sbowerma wrote:
Hi Justin,
Thanks for your response. I did see the g_angle tool, but doesn't it have a
similar limitation as AMBER's ptraj? From what I can see, I would still
need to script out an index file for every single dihedral atom set of
interest (which is all of
Hi Justin,
Thanks for your response. I did see the g_angle tool, but doesn't it have a
similar limitation as AMBER's ptraj? From what I can see, I would still
need to script out an index file for every single dihedral atom set of
interest (which is all of them and I have over 1k residues). Whil
Yes indeed - and thanks to Alexey and Tom for the .rtp/hdb and .itp files,
respectively! Much appreciated.
On Apr 12, 2014, at 1:18 AM, Alexey Shvetsov wrote:
> В письме от 11 апреля 2014 14:11:09 пользователь Justin Lemkul написал:
>> On 4/11/14, 1:43 PM, Stephen N. Floor wrote:
>>> Hi groma
On 4/14/14, 4:33 PM, sbowerma wrote:
Hello all,
I am currently looking at the g_chi analysis tool. I would like to create a
time distribution of dihedral angle values for a dna-protein system, with
the end-goal of using this distribution in a mutual information calculation.
Unfortunately, I s
Hello all,
I am currently looking at the g_chi analysis tool. I would like to create a
time distribution of dihedral angle values for a dna-protein system, with
the end-goal of using this distribution in a mutual information calculation.
Unfortunately, I see that the g_chi tool is limited to onl
Dear Gmxers,
I did a simulation of 2048 liquid water and vapour interface using
gromacs.I need to
identify the dynamics of the molecules on the interface for which I am
trying to use g_select
but i am not sure how to go about it.
In principle the box length along z-axis is 120 A and the interfac
Dear users,
I try to calculate Hydrogen Bonding lifetimes with g_hbond, but I get a
negative value for the forward time.
I searched through the mailing list, and it reports that we should look to
the ACF graph. In my case it falls dramatically to zero(I have attached it
to this mail).
How can I
There will be no support for MC in GROMACS 5.0
Mark
On Mon, Apr 14, 2014 at 4:20 PM, xiao wrote:
> Dear Gromacs users,
>
>
> I am studying the dimerization of two organic molecules. I hope i can
> simulate the dimerization process by using Monte Carlo method. I noticed
> that the MC script is
On 4/14/14, 10:03 AM, MUSYOKA THOMMAS wrote:
Dear users,
I am doing a 10 ns protein-ligand simulation and would like to determine
the hydrogen and hydrophobic interactions per each ns and the participating
amino acid residues.
How do I go about this?
g_hbond and g_mindist, combined with sui
On 4/14/14, 10:20 AM, xiao wrote:
Dear Gromacs users,
I am studying the dimerization of two organic molecules. I hope i can simulate
the dimerization process by using Monte Carlo method. I noticed that the MC
script is in the latest version of gromacs 5.0, but there is no such manual on
t
Dear Gromacs users,
I am studying the dimerization of two organic molecules. I hope i can simulate
the dimerization process by using Monte Carlo method. I noticed that the MC
script is in the latest version of gromacs 5.0, but there is no such manual on
that, and the latest manual is 4.6. Can
Dear users,
I am doing a 10 ns protein-ligand simulation and would like to determine
the hydrogen and hydrophobic interactions per each ns and the participating
amino acid residues.
How do I go about this?
Thank you.
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Thank you for your reply. I will look into freezegrps, it might be just
what I need.
Question 1) was more related to whether needing such large numbers might
be indicative of a problem with my calculation, given that they are 5
orders of magnitude larger than the default. Of course I would exp
On 4/14/14, 8:45 AM, Miguel Caro wrote:
Hi all,
I am trying to do an MD simulation of a small hexagonal box where I need some of
the atoms to stay fixed. This is because I am mixing ab initio and classical MD
and some of the atoms in my system should remain within the configuration
predicted b
Hi all,
I am trying to do an MD simulation of a small hexagonal box where I need
some of the atoms to stay fixed. This is because I am mixing ab initio
and classical MD and some of the atoms in my system should remain within
the configuration predicted by DFT.
As far as I know, GROMACS only
Yep, seems right.
Mark
On Mon, Apr 14, 2014 at 2:00 PM, Dr. Vitaly Chaban wrote:
> seems I achieved that with
>
> 1 & ! 2
>
>
>
> Dr. Vitaly V. Chaban
>
>
> On Mon, Apr 14, 2014 at 1:52 PM, Dr. Vitaly Chaban
> wrote:
> > Hi Everyone -
> >
> > What is my command line if I need to exclude sites
seems I achieved that with
1 & ! 2
Dr. Vitaly V. Chaban
On Mon, Apr 14, 2014 at 1:52 PM, Dr. Vitaly Chaban wrote:
> Hi Everyone -
>
> What is my command line if I need to exclude sites belonging to group
> #2 from group #1?
>
> Thank you.
>
>
> Dr. Vitaly V. Chaban
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Gromacs Users mailing
Hi Everyone -
What is my command line if I need to exclude sites belonging to group
#2 from group #1?
Thank you.
Dr. Vitaly V. Chaban
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