Thanks for the reply.
I'm trying to test out a theory that enzymes gain "heat" from their
substrate after the catalytic reaction finishes, thus my plan to heat up
the active site. Is there a better approach to testing this theory?
How would I specify the groups?
Felix
>
>
> On 5/5/17 6:56 PM,
On 5/5/17 6:56 PM, Felix Y Yang wrote:
Good afternoon,
I am a graduate student working at UCSD, and currently working on a few
simple proteins like beta-amylase, insulin, and triosephosphate isomerase
in gromacs. I'm fairly new to protein simulations in general, and I would
like to know if the
Good afternoon,
I am a graduate student working at UCSD, and currently working on a few
simple proteins like beta-amylase, insulin, and triosephosphate isomerase
in gromacs. I'm fairly new to protein simulations in general, and I would
like to know if there is a way to identify and isolate the act
On 5/5/17 10:04 AM, Hannes Loeffler wrote:
On Fri, 5 May 2017 15:09:09 +0200
Pallavi Banerjee wrote:
I intend to perform thermodynamic integration of my system, but not to
calculate the free energy. I want to gradually increase the radius of
the carbon atoms of the alkyl chains of my lipid m
On 5/5/17 1:37 PM, Alex wrote:
Dear Gromacs user,
I want to study the interaction between a nanoparticle(5 nm diameter) and
some heptapeptide around the nanoparticle in aqueous solution. I put
the nanoparticle
in the center of a box and the rest are around it.
I was wondering if I should use P
Hi,
Topologies are specific to force fields. You still need to go and
understand how they should be used. And probably to choose your force field
and topology generation method based on what science you want to achieve.
:-)
Mark
On Fri, 5 May 2017 20:49 Syed Azeem wrote:
> Hey Mark,
>
> Thanks
Hey Mark,
Thanks for the reply. I even tried other force fields, which yielded
the same errors. For Gromos 53a6 ff, "No default Ryckaert-Bell types"
was included in the error.
> Hi,
>
> grompp will always need angle type definitions for the angles in the .itp
> file - they have to either be in th
Dear Gromacs user,
I want to study the interaction between a nanoparticle(5 nm diameter) and
some heptapeptide around the nanoparticle in aqueous solution. I put
the nanoparticle
in the center of a box and the rest are around it.
I was wondering if I should use PBC (periodic boundary condition) in
Gromacs can be compiled with GCC 6 without problem.
The problem is that CUDA, up to version 8.0.61 at least, doesn't support
GCC > 5
On 05/05/2017 06:51 PM, De Crisci, Antonio (NRCan/RNCan) wrote:
> Hello,
>
> Would like to use Gromacs CPU/GPU on my Ubuntu 17.04 system. I have been
> following
Hello,
Would like to use Gromacs CPU/GPU on my Ubuntu 17.04 system. I have been
following these instructions, and has been working well till the 'build and
install' part:
http://www.nvidia.com/object/gromacs-installation.html
The problem its saying is that Gromacs doesn't support GNC/GCC versi
Hi,
That's a bug, please report it. It looks like the -nofit option should mean
-s is optional in your case, but the implementation is not great.
Mark
On Fri, May 5, 2017 at 4:57 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Dear users:
>
>
> I'm writing to check that I understa
Thank you!
On 05.05.2017 16:05, Mark Abraham wrote:
> Hi,
>
> It really doesn't do much.
> http://manual.gromacs.org/documentation/2016/user-guide/mdp-options.html#bonds
> covers
> it. (Background: people expect that output is written with constraints
> satisfied, we write the checkpoint at the s
In reply to Mark's comment, it used to be that one could specify separate LJ
1-4 interactions as he suggests, but there is no route to do this for Coulmb
1-4 scaling. Perhaps that haas changed in more recent versions of gromacs. If
not, you might consider a variant of the approach that we used a
Dear users:
I'm writing to check that I understand the "(Opt.)" notification in gmx * -h
output.
For example, gmx cluster -h lists a topology as optional:
-s [<.tpr/.gro/...>] (topol.tpr) (Opt.)
But without a topology the evaluation crashes:
GROMACS: gmx cluster, VERSION
On Fri, 5 May 2017 15:09:09 +0200
Pallavi Banerjee wrote:
> I intend to perform thermodynamic integration of my system, but not to
> calculate the free energy. I want to gradually increase the radius of
> the carbon atoms of the alkyl chains of my lipid molecules. This is
> because I could see a
Hi,
It really doesn't do much.
http://manual.gromacs.org/documentation/2016/user-guide/mdp-options.html#bonds
covers
it. (Background: people expect that output is written with constraints
satisfied, we write the checkpoint at the same time for convenience and
efficiency, the initial simulation par
Hello,
This might be a trivial question for most of you but can someone give me
more detail about what the 'continuation' flag in the .mdp settings
does? The manual does not include a lot of information on that.
Best regards,
Daniel
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Hi gromacs users,
I intend to perform thermodynamic integration of my system, but not to
calculate the free energy. I want to gradually increase the radius of the
carbon atoms of the alkyl chains of my lipid molecules. This is because I
could see a hole forming in my lipid bilayer along the edges
Hi,
As you can see in the documentation of the topology file format in chapter
5 of the reference manual, whether intra-molecular "pair" interactions for,
say, 1-4 interactions have parameters generated from the normal non-bonded
interactions (perhaps via scaling), or not is a property of the forc
Hi,
Extensibility, and availability of quality automated tool support for that
are things that should go into your choice of force field. There may be
such for OPLS (I literally don't know). You need to choose an appropriate
force field; that means you need one that has citrate, or can be extended
Hi,
grompp will always need angle type definitions for the angles in the .itp
file - they have to either be in the force field already, or added to it.
If they are not present in amber99sb-ildn, then you need to understand how
the topologies were generated and how they are intended to be used in o
Hi,
On Fri, May 5, 2017 at 1:44 PM Patel, Hershna wrote:
>
> Dear Gromacs users
>
>
> I am trying to do energy minimisation of a protein-ligand complex. When
> visualising the output trajectory and .gro file, the structure of the
> ligand becomes distorted. The same thing happens when constraini
HI,
It will be very helpful if you can provide the log file and I think this is
a note by gromacs and not a warning.
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Dear Gromacs users
I am trying to do energy minimisation of a protein-ligand complex. When
visualising the output trajectory and .gro file, the structure of the ligand
becomes distorted. The same thing happens when constraining all-bonds during
EM. After running grompp, there is this note:
Hi all,
I'm trying to simulate a Protein-Peptide docked complex.
I used Amber99sb-ildn ff with TIP3P. Since mine is a docked complex,
two separate topology and position restraint files were created as
chains A & B, automatically.
When I tried to generate the .tpr file for adding ions to the syste
I'm using the OPLS ff but I can't seem to find a tool in which I can generate
topology for this force field. I looked up the ones recommended on GROMACS but
had no luck. I also have SWISSParam but that is for CHARMM.
Akash
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