Hi guys,
What is the best way of calculating how far a residue has traveled from its
starting position during a simulations?
Thanks
Natalie
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
Hi,
I know there have been many threads talking about parameterization of novel
molecules for simulations within gromacs, but I just wanted to know if anyone
had done any parameterization of myristic acid, as I intend to begin
simulations on a protein that is myristolated and figured I'd
] Potential Energy Landscape
On 21/11/2011 10:36 PM, Natalie Stephenson wrote:
I have performed force pulling experiments on a protein with both Gromacs MD
simulations and experimentally with AFM. The problem I'm facing with the
data is the difference between the loading rates of the two approaches
to
experimental data dispite the loading rate differences would be GREATLY
appreciated!!
Thanks once again!!
Natalie
Natalie Stephenson, B.Sc
PhD Research Associate
Manchester Interdisciplinary Biocentre
131 Princess Street
Manchester
M1 7DN
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: 21 October 2011 13:25
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Potential Energy Landscape
Natalie Stephenson
the least in the last 7 years ... so getting back into it is proving
more confusing!
Natalie
Natalie Stephenson, B.Sc
PhD Research Associate
Manchester Interdisciplinary Biocentre
131 Princess Street
Manchester
M1 7DN
x65816
I was recently told in passing that it would be possible to construct a
'potential energy landscape' from the simulations I have performed. This way I
could remove any loading rate differences between simulations and experimental
force experiments I've been performing ... however I cannot find
pulling
on both termini if this is in fact the case?
Thanks
Natalie
Natalie Stephenson, B.Sc
PhD Research Associate
Manchester Interdisciplinary Biocentre
131 Princess Street
Manchester
M1 7DN
x65816
the fact that this
domain is very firmly in contact with it's adjacent domain?
Thank you for your help with this matter.
Kind regards,
Natalie
Natalie Stephenson, B.Sc
PhD Research Associate
Manchester Interdisciplinary Biocentre
131 Princess
. Is this possible?
Thanks
Natalie
Natalie Stephenson, B.Sc
PhD Research Associate
Manchester Interdisciplinary Biocentre
131 Princess Street
Manchester
M1 7DN
x65816
--
gmx-users mailing listgmx-users
Thanks loads! That helps loads!
Natalie
Natalie Stephenson, B.Sc
PhD Research Associate
Manchester Interdisciplinary Biocentre
131 Princess Street
Manchester
M1 7DN
x65816
to be functioning
fine. What is it I've missed?
Can anyone shed any light on my (probably completely stupid) problem?!
Thanks loads,
Natalie
Natalie Stephenson, B.Sc
PhD Research Associate
Manchester Interdisciplinary Biocentre
131 Princess Street
...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: 16 May 2011 15:56
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Command Not Found
Natalie Stephenson wrote:
Hi All,
Sorry to bug you all about this - it's been mentioned a few times but I
can't find an answer
Subject: Re: [gmx-users] Command Not Found
Natalie Stephenson wrote:
Sorry for the confusion - didn't mean I'd used a wildcard when typing the
commands ... just meant I get that response for both commands.
They're an add on created from a the Molecular BioMechanics group
(http://projects.eml.org
Hi,
I was wondering if anyone new a way to run mdrun commands through a condor
system. I've been told by the people that run our system that unless I can
split it into seperate threads then I would not be able to run it as a job,
because it would just get stopped in the morning - which from
Hi,
I've been having a problem with the pull simulation. After the simulation is
complete, I use trjconv to separate the pull file into seperate .gro's and load
this into VMD. When I view it in VMD as the 'video' continues parts of amino
acids within the protein structure seem to jump a
Subject: Re: [gmx-users] Problems with pull simulation output - VMD shows
broken up groups
Justin A. Lemkul wrote:
Natalie Stephenson wrote:
Hi,
I've been having a problem with the pull simulation. After the
simulation is complete, I use trjconv to separate the pull file into
seperate
of Justin A. Lemkul [jalem...@vt.edu]
Sent: 10 December 2010 13:52
To: Gromacs Users' List
Subject: Re: [gmx-users] Invalid atom number 101717 in indexfile
Natalie Stephenson wrote:
Hi,
There are 101987 atoms in my system (2206 from my protein and the rest from
solvent and ions). The index file
Hi,
I've come across this error when performing grompp of my pull files before an
afm simulation. I'm not really sure I understand why it's saying it ... I've
checked over my index file and the atom is part of the solvent I've solvated
the box with during genbox commands.
The input on the
Hey,
I've been performing a pull simulation of a protein, all seems to work fine
however after I convert the .xtc file into seperate .gro files and load those
into VMD to visualise the simulation something weird happens. Every 50 frames
or so a random bond within the backbone of the protein
users
Subject: Re: [gmx-users] Pull simulation odditites when viewed in VMD
Natalie Stephenson wrote:
Hey,
I've been performing a pull simulation of a protein, all seems to work
fine however after I convert the .xtc file into seperate .gro files and
load those into VMD to visualise the simulation
Hi ...
Just wondering if there's a way, during pulling simulations, to immobilise say
the C-terminus of the protein.
I've been running through the 'Umbrella Sampling' tutorial with my own protein.
Within this tutorial the ChainB is used as the immobile reference - so it is
this that is
Hi everyone,
I was hoping you could clear up a problem I'm having when performing energy
minimisation. I'm following the instructions from one of the tutorials
(Justin's Umbrella Sampling) with my own protein, however, this time when I try
to perform the energy minimisation it throws out this
On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson
natalie.stephen...@postgrad.manchester.ac.ukmailto:natalie.stephen...@postgrad.manchester.ac.uk
wrote:
Hi everyone,
I was hoping you could clear up a problem I'm having when performing energy
minimisation. I'm following the instructions from one
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk]
Sent: 22 September 2010 13:02
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Energy minimisation problems
for GROMACS users
Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and
topology file not matching.
Natalie Stephenson wrote:
Ok ... think I've worked out what's happened ...
There were two 'SOL' groups. So when replacing solvent with ions it has
added double the amount
Hi,
I'm a complete novice when it comes to using any kind of command
prompt based programmes and hadn't even heard of Linux until my
supervisor wanted me to use gromacs ... so needless to say I'm running
into a few problems!!
I've managed to perform all the generic energy minimisations
Quoting Justin A. Lemkul jalem...@vt.edu:
Natalie Stephenson wrote:
Hi,
I'm a complete novice when it comes to using any kind of command
prompt based programmes and hadn't even heard of Linux until my
supervisor wanted me to use gromacs ... so needless to say I'm
running into a few
28 matches
Mail list logo
