On 28/03/2012 2:14 PM, Davide Mercadante wrote:
Thank you for the prompt reply.! Indeed, I am using Gromacs version
4.5.5 compiled in double-precision and I am running the analysis on a
MacBook PRO.
I tried to open an issue at http://redmine/gromacs.org but it asks me
for login name and
On 28/03/2012 6:52 PM, Jernej Zidar wrote:
Hi.
After successfully importing a CHARMM-generated PDB file to GROMACS
I set out to do some short simulations. While all calculations
finished without a problem if everything but the water molecules were
fixed.
Removing the position restraints
On Wed, March 28, 2012 00:53, gmx-users-requ...@gromacs.org wrote:
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Hi all
I have never posted to the mailing list before but it has proven very
helpful in the past.
I'm looking for the 45A4 force field. I've been asking Mr. Google but so
far I haven't had any luck locating it. This is I imagine probably down to
the wrong keywords or something
I want to do
On Wed, Mar 28, 2012 at 16:17, gmx-users-requ...@gromacs.org wrote:
See the warning in genrestr -h.
If all you're doing is adding a single atom of position restraint per
moleculetype, you can do that by hand faster than using make_ndx and
genrestr and adding the #include.
Mark
This in
Thanks for your inputs.
I have checked the coordinate file thoroughly and the order of atoms
are same as defined in the [molecules] directive.
I really do not able to find out the source of the error.
On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul jalem...@vt.edu wrote:
Biswajit Gorai wrote:
Dear All,
Currently is it possible to run MD at a constant pH value?
I am looking forward to getting a reply from you.
Cheers,
Acoot
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Dear All,
Can you show me a webpage to calculate the Tm (melting temperature) of a
protein (complex) by Gromacs?
Cheers,
Acoot
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Please search the archive at
Acoot Brett wrote:
Dear All,
Currently is it possible to run MD at a constant pH value?
The concept of pH is not well defined in MD simulations. In normal MD, you
can't transfer protons and you can't explicitly model the actual hydronium
concentration without making your box
bipin singh wrote:
Thanks for your inputs.
I have checked the coordinate file thoroughly and the order of atoms
are same as defined in the [molecules] directive.
I really do not able to find out the source of the error.
Looking closer at the error, what's happening is your octanol molecule
Marc Gordon wrote:
Hi all
I have never posted to the mailing list before but it has proven very
helpful in the past.
I'm looking for the 45A4 force field. I've been asking Mr. Google but so
far I haven't had any luck locating it. This is I imagine probably down
to the wrong keywords or
Dear All,
In http://www.gromacs.org/Documentation/How-tos/REMD;, the first sentence is
Replica-Exchange Molecular Dynamics (REMD) is a technique used to enhance
sampling relative to a standard molecular dynamics simulations by allowing
systems of similar potential energies to sample
Dear All,
Does anyone can make an introduction on the differences among the following
force fields for protein? Which are much easy to be accepted for publication
purpose?
Cheers,
Acoot
1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell
On 2012-03-28 13:02, Acoot Brett wrote:
Dear All,
Does anyone can make an introduction on the differences among the
following force fields for protein? Which are much easy to be accepted
for publication purpose?
Try reading some literature. Search for protein force field simulation.
Acoot Brett wrote:
Dear All,
In http://www.gromacs.org/Documentation/How-tos/REMD;, the first
sentence is Replica-Exchange Molecular Dynamics (REMD) is a technique
used to enhance sampling relative to a standard molecular dynamics
simulations
Dear Gromacs Users!
I have some questions about PCA implemented in Gromacs.
1- I want to increase amplitude of the motions seen on the selected PCs but
I can't found scalling factor option for that.
2- I have calculated MD trajectory for my protein. From this trajectory I
want to find some
Mark,
This sounds like I use very small forces but expect reasonable effect. But
I've applied different forces with step-by-step increasing of force
constants ( from very softest comparable with the thermal motion ( 0.1 kj
mol nm-2) to relatively hight (10). As the consequence I've observed
On 28/03/2012 7:39 PM, Jernej Zidar wrote:
On Wed, Mar 28, 2012 at 16:17,gmx-users-requ...@gromacs.org wrote:
See the warning in genrestr -h.
If all you're doing is adding a single atom of position restraint per
moleculetype, you can do that by hand faster than using make_ndx and
genrestr and
On 28/03/2012 9:42 PM, Justin A. Lemkul wrote:
Acoot Brett wrote:
Dear All,
Currently is it possible to run MD at a constant pH value?
The concept of pH is not well defined in MD simulations. In normal
MD, you can't transfer protons and you can't explicitly model the
actual hydronium
On 28/03/2012 10:48 PM, James Starlight wrote:
Mark,
This sounds like I use very small forces but expect reasonable effect.
But I've applied different forces with step-by-step increasing of
force constants ( from very softest comparable with the thermal motion
( 0.1 kj mol nm-2) to
Hi James,
1- I want to increase amplitude of the motions seen on the selected PCs but
I can't found scalling factor option for that.
The analysis gives you the amplitudes that are in your trajectory. Why
do you want to amplify them to something probably non-physical?
2- I have calculated MD
Oh awesome. Thanks so much for this.
I've never worked with GROMOS or gromacs themselves. I'm going to need to
look up whether or not it is possible to use these files to generate files
in the gromacs format required as input for NAMD now but at least having
access to the force fields puts me
Marc Gordon wrote:
Oh awesome. Thanks so much for this.
I've never worked with GROMOS or gromacs themselves. I'm going to need
to look up whether or not it is possible to use these files to generate
files in the gromacs format required as input for NAMD now but at least
having access to
bipin singh wrote:
Thanks again
For the record, I didn't ask that you send me your files so I could troubleshoot
for you. Luckily for you I'm in a charitable mood this morning, so I took a look ;)
Your problem is that you have a [molecules] directive in oct.itp. Please refer
to the
You could have a look at
Donnini et al, JCTC 7 (2011), 1962-1978
And with teh code available from
http://www.mpibpc.mpg.de/home/grubmueller/projects/Methods/ConstpH/index.html
give it a try for your problem.
Gerrit
1. on MD at constant pH (Acoot Brett)
Dear All,
Currently is it
A lot of thanks to your charitable mood now the things has been resolved :) .
Thanks again.
On Wed, Mar 28, 2012 at 18:24, Justin A. Lemkul jalem...@vt.edu wrote:
bipin singh wrote:
Thanks again
For the record, I didn't ask that you send me your files so I could
troubleshoot for you.
Hi Tsjerk,
Thanks for all the clarifications about PCA you make on the mailing list! I
have a question about the commandlines you wrote. Why do you use the .tpr
file with the -s flag? Is it because you want to compare the
mass-wheighted covariance matrices? I use to calculate the covariance
Ah well no worries. I will delve back into the gromacs and NAMD user guides
and see what I can dig up with regards to getting these GROMOS files
working through NAMD.
Thanks again for the help you have given me.
Marc
On Wed, Mar 28, 2012 at 4:19 PM, Justin A. Lemkul jalem...@vt.edu wrote:
True. Even more so if the position restraints file can be generated with basic
Bash commands in under a minute.
Jernej
On 28. mar. 2012, at 20:16, gmx-users-requ...@gromacs.org wrote:
It's pretty rare to have more than a handful of [moleculetype] sections,
each of which would want
Hi Thomas,
Thanks for all the clarifications about PCA you make on the mailing list!
Thank you for the appreciation :)
I have a question about the commandlines you wrote. Why do you use the .tpr
file with the -s flag? Is it because you want to compare the
mass-wheighted covariance matrices?
Dear:
I am using gromacs for membrane simulation (under CHARMM36 FF) which
contains around 80,000 atoms. I've submitted over 200 CPU in the cluster
for such system with 2 fs time step. And what really astonished is that the
efficiency for such simulation is only 3ns/day. I am wondering what
Albert wrote:
Dear:
I am using gromacs for membrane simulation (under CHARMM36 FF) which
contains around 80,000 atoms. I've submitted over 200 CPU in the cluster
for such system with 2 fs time step. And what really astonished is that
the efficiency for such simulation is only
Иимяа Фаамиилиияа wrote:
Hi,
I am trying construct homopolymer from non-standard monomers .
I have pdb, itp and gro files for monomer and constructed pdb file for polymer.
I can put them in corresponding top/forcefield.ff directory.
But how I can get itp and gro files for polymer (for
Hi Albert,
You are doing neighboursearching every step! So every step all 200
CPUs need to know the how and what of all the other 199. Imagine the
communication overhead. Furthermore, you have 400 atoms per CPU
(neglecting the PME dedication). That will also make communication a
bottle neck.
On Wed, 28 Mar 2012 17:31:47 +0200
Albert mailmd2...@gmail.com wrote:
I am using gromacs for membrane simulation (under CHARMM36 FF) which
contains around 80,000 atoms. I've submitted over 200 CPU in the
cluster for such system with 2 fs time step. And what really
astonished is that the
Hi Tsjerk!
First, I'd like also thanks you for your help.
Today I tried to make PCA of my X-ray data as well as comparison between
results of such PCA and EDA ( PCA wich is based on the MD trajectory of the
same protein).
In generaly I have no any problems with the X-ray PCA but I've forced
Hi Marc,
Though I never came across ready-to-use files for Gromos 45A4, you can
for sure get all the parameters for carbohydrates from [1] and
transfer them into a Gromacs format (make sure to convert all the
units).
Searching briefly for the term 45A4 in [2] lets me believe, that the
parameters
Mark,
thanks for explanation again.
28 марта 2012 г. 16:04 пользователь Mark Abraham
mark.abra...@anu.edu.auнаписал:
That can mean big restraint forces and tiny integration steps and lots of
tweaking and praying.
Yes I think this aproach could be usefull in my case. Actually I want to
Does some one know of a way to get g_rms or g_rmsf to write out the x, y, and z
components of the rms(f) for each atom/residue separately?
Thanks.
Patrick L. Wintrode
Department of Pharmaceutical Sciences
University of Maryland
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gmx-users mailing listgmx-users@gromacs.org
I believe that rmsf can compute anisotropic b-factors, but have not tried it
myself.
Erik
28 mar 2012 kl. 22.32 skrev patrick wintrode:
Does some one know of a way to get g_rms or g_rmsf to write out the x, y, and
z components of the rms(f) for each atom/residue separately?
Thanks.
On 29/03/2012 5:53 AM, James Starlight wrote:
Mark,
thanks for explanation again.
28 ? 2012 ?. 16:04 Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au ???:
That can mean big restraint forces and tiny integration steps and
lots of tweaking
Dear GMCS users
Hi. Does anyone know if MD at 2K is feasible?
Thanks,
Best regards,
Asaf
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Erik Marklund [er...@xray.bmc.uu.se]
Sent: Wednesday, March 28, 2012 10:37 PM
To:
On 29/03/2012 9:39 AM, Asaf Farhi wrote:
Dear GMCS users
Hi. Does anyone know if MD at 2K is feasible?
Please start new email threads rather than hijacking old ones.
I doubt anybody knows the answer to your question. Force fields are
parameterized to reproduce data at around 300K. I
At that temperature most matter is going to be a plasma, not many bonds to be
simulated and a lot of free electrons.
Warren Gallin
On 2012-03-28, at 4:43 PM, Mark Abraham wrote:
On 29/03/2012 9:39 AM, Asaf Farhi wrote:
Dear GMCS users
Hi. Does anyone know if MD at 2K is feasible?
I am using gromacs for membrane simulation (under CHARMM36 FF) which
contains around 80,000 atoms. I've submitted over 200 CPU in the cluster
for such system with 2 fs time step. And what really astonished is that the
efficiency for such simulation is only 3ns/day. I am wondering what
Thanks Erik,
In case I run my simulations on 4 nodes, please let me know what do I have
to add to the command to start MPI? I have used the commands:
*grompp -f NVT_50ns.mdp -o NVT_50ns.tpr -c NVT_20ns.g96 -p topol.top
mdrun -s NVT_50ns -o NVT_50ns -c NVT_50ns -x NVT_50ns -e NVT_50ns -g
NVT_50ns
Hi,
I was trying to calculate the pressure tensors for one of my solid crystal
systems. I notice that g_energy does have this option---pressure xx,
pressure yy and pressure zz, however the results seem to be a function of
running time. How can I extract information about pressure tensor at
Dear GMCS users
Hi. Does anyone know if MD at 2K is feasible?
Aggregate state, not temperature, matters if you want to discuss
potential models applicability.
I believe at ~10,000K one can get quite realistic results for the
gaseous phase of certain high-melting substances like CaO or
On 29/03/2012 12:25 PM, cuong nguyen wrote:
Thanks Erik,
In case I run my simulations on 4 nodes, please let me know what do I
have to add to the command to start MPI? I have used the commands:
/grompp -f NVT_50ns.mdp -o NVT_50ns.tpr -c NVT_20ns.g96 -p topol.top
mdrun -s NVT_50ns -o NVT_50ns
I disagree.
What one is generally trying to obtain with elevated temperatures is
enhanced sampling, not temperature-dependent properties. I believe
that even TIP4P-EW is not very good at getting the properties of water
correct at 600 K, temperatures that are commonly used during replica
On 29/03/2012 11:03 AM, Dr. Vitaly V. Chaban wrote:
I am using gromacs for membrane simulation (under CHARMM36 FF) which
contains around 80,000 atoms. I've submitted over 200 CPU in the cluster
for such system with 2 fs time step. And what really astonished is that the
efficiency for such
Please start a new thread for a new topic.
T.
On Thu, Mar 29, 2012 at 12:39 AM, Asaf Farhi asaf.fa...@weizmann.ac.ilwrote:
Dear GMCS users
Hi. Does anyone know if MD at 2K is feasible?
Thanks,
Best regards,
Asaf
--
*From:*
Hi Patrick,
You can extract the diagonal from the covariance matrix generated with
g_covar (-ascii). That is equal to the RMSF per atom-coordinate.
Cheers,
Tsjerk
On Wed, Mar 28, 2012 at 10:32 PM, patrick wintrode pat_w...@yahoo.comwrote:
Does some one know of a way to get g_rms or g_rmsf to
Hey,
Hotter than the sun only goes for the surface. The core and the corona
are much hotter. Whether electrons get separated from nuclei or
nuclear fusion should start to occur also depends on pressure... But
the question itself pertains to the code and the application of
Newton's equations of
HI Gromacs Friends,
I complete one simulation for 4 different molecule placed
apart
in box of dimension 4 4 4 ..
when I used the trajectory I saw the one molecule interact with each other
but they are
getting broken because of box..(Some part protruding from other side).
To see
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