Dear all Gromacs user,
I am trying to perform the Normal Mode Analysis protein-DNA complex
in vacuum. As the complex is highly negative charge (-163)I performed
the energy minimization of complex in water (to neutralize the
complex). After I get the completely minimized complex, again I have
do
Hello.
I am trying to do a Normal Mode Analysis of a polymer in water. I am running my
minimization right now with -DFLEXIBLE defined.
How do I exclude the water from the analysis. I only want the analysis done on
the polymer.
Dan Sponseller
PhD student, George Mason University
--
Gromacs Use
Dear all,
I wonder if there is anywhere I can know the details of mdp files used for
normal mode analysis.
I understand from the maunal that it needs steepest descent, conjugate
gradient, l-bfgs, nm in "md" options consecutively,
but I am not sure about other parameters set in these different s
Hello All,
I am simulating two proteins in solution and would like to perform Normal
Mode Analysis on trajectory snapshots.
I take one particular frame in the trajectory and minimize it, followed by
mdrun for normal mode analysis. However I am getting constraint errors in
each of the two steps -
1
?Hello,
Currently I am trying to perform a normal mode analysis on my pdb file using
Gromacs 2019.3.
But during energy minimalisation I can't seem te get my energy low enough. it
remains around 10^01-10^00.
I used the attached mdp-files.
Am I doing something wrong? If so, what am I doing wr
Dear users,
I am trying to do NMA
First i did energy minimization using .mdp file with conjugate gradient
method,
Next i calculated hessian matrix by using integrator = nm
Then i calculated the eigen vectors from 7 to 100 using g_nmeig
to analyze eigen vectors i use the comm
Dear gromacs users,
I am interested in normal mode analysis, but i have no idea about the time
needed for NMA compared with the regular MD.
My friend who uses NAMD, and he told me that the NMA took much time. The reason
may be that he used all-atom force field, can anyone tell me whether gro
Dear all,
I am trying to perform the Normal Mode Analysis protein in water.
Here is the .mdp file I am using:
integrator = nm; time step
nsteps = 10 ; number of steps
nstlist = 10; update pairli
Hi Rahul,
Did you make the vacuum minimization with a double-precision version
of gromacs using the L-BFGS algorithm? From the protocol you described it
seems you didn't do it..
What was the maximum force after the minimization? (check the .log
file)
I hope it helps,
Leandro.
On Sat,
Perhaps, trjconv -- to delete all you do not need?
On Wed, Oct 14, 2015 at 2:49 PM, Dan Sponseller wrote:
> Hello.
>
> I am trying to do a Normal Mode Analysis of a polymer in water. I am
> running my minimization right now with -DFLEXIBLE defined.
>
> How do I exclude the water from the a
Hi all
I am running a normal mode analysis on a system with 1.05 million atoms without
solvent.
I performed extensive double precision energy minimization using conjugate
gradient (more than
14 days using 1024 processor). and my final values are:
Potential Energy = -8.54191598792831e+06
Max
Den 2019-10-16 kl. 23:31, skrev Adip Jhaveri:
Hello All,
I am simulating two proteins in solution and would like to perform Normal
Mode Analysis on trajectory snapshots.
I take one particular frame in the trajectory and minimize it, followed by
mdrun for normal mode analysis. However I am gettin
Thank you for the response.
But how will the system be affected when I remove the constraints? I am
trying to get a measure of the entropy by the normal mode analysis, so will
removing the constraints lead to an incorrect estimation?
Regards,
Adip
On Thu, Oct 17, 2019 at 4:06 AM David van der Spo
Yes I used double precision for everything.
-Katrien
From: Smith, Micholas D.<mailto:smit...@ornl.gov>
Sent: woensdag 26 februari 2020 13:39
To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Normal mode analysis
Is your build of GROMACS
for Molecular Biophysics
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Katrien Clerx
Sent: Wednesday, February 26, 2020 6:31 AM
To: gmx-us...@gromacs.org
Subject: [EXTERNAL] [gmx-users] Normal mode analysis
?Hello,
Currently I am trying
National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Katrien Clerx
Sent: Wednesday, February 26, 2020 7:52 AM
To: gmx-us...@gromacs.org
Subject: [EXTERNAL] Re: [gmx-users] Normal mode analysis
>
Sent: woensdag 26 februari 2020 14:10
To: Katrien Clerx<mailto:katrien.cl...@student.kuleuven.be>;
gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Normal mode analysis
Hmmm
How did you prepare the structure? Also, attachments are stripped from e
Biophysics
From: Katrien Clerx
Sent: Wednesday, February 26, 2020 8:29 AM
To: Smith, Micholas D. ; gmx-us...@gromacs.org
Subject: [EXTERNAL] RE: [gmx-users] Normal mode analysis
My structure does not contain any ions. Here are the commands that I used:
gmx_d
>From g_nmeig -h:
An ensemble of structures can be generated from the eigenvectors with
g_nmens.
Cheers,
Tsjerk
On Mon, Nov 25, 2013 at 5:05 PM, Sathish Kumar wrote:
> Dear users,
>
>I am trying to do NMA
>
> First i did energy minimization using .mdp file with conjugate g
Is that ensemble of structures are related to each eigen vector or total
eigen vectors.
If i want to see the motion of seventh eigen vector how can i get?
On Mon, Nov 25, 2013 at 9:50 PM, Tsjerk Wassenaar wrote:
> From g_nmeig -h:
>
> An ensemble of structures can be generated from the eigenve
Hi Sathish,
Have you tried reading the g_nmens manpage or the manual?
Cheers,
Tsjerk
On Mon, Nov 25, 2013 at 6:00 PM, Sathish Kumar wrote:
> Is that ensemble of structures are related to each eigen vector or total
> eigen vectors.
>
> If i want to see the motion of seventh eigen vector how ca
, etc...
Stephan Watkins
Gesendet: Montag, 25. November 2013 um 17:05 Uhr
Von: "Sathish Kumar"
An: "Discussion list for GROMACS users"
Betreff: [gmx-users] Normal Mode Analysis
Dear users,
I am trying to do NMA
First i did energy minimization using .mdp file with conjuga
Hi Fugui,
It uses whatever you put into it. You could try Martini. But should you
want to? It sounds like you should do a bit more background reading.
Cheers,
Tsjerk
On Nov 25, 2013 10:45 PM, "xiao" wrote:
Dear gromacs users,
I am interested in normal mode analysis, but i have no idea about
; *An:* "Discussion list for GROMACS users"
> *Betreff:* [gmx-users] Normal Mode Analysis
> Dear users,
>
> I am trying to do NMA
>
> First i did energy minimization using .mdp file with conjugate gradient
> method,
>
> Next i calculated hessian matrix by using
Sorry,
Your correct. Thanks for correcting me. I dont want to send people off on tangents, and thus appologise.
Stephan
Gesendet: Dienstag, 26. November 2013 um 07:43 Uhr
Von: "Tsjerk Wassenaar"
An: "Discussion list for GROMACS users"
Betreff: Re: [gmx-users]
r GROMACS users"
Betreff: Re: [gmx-users] Normal Mode Analysis
Hi Stephen,
You're confusing NMA with PCA.
Cheers,
Tsjerk
On Tue, Nov 26, 2013 at 6:30 AM, lloyd riggs wrote:
> I don't know your energy break down, if you look at frames with g_anaeig
> using -first and -last to
:43 Uhr
> *Von:* "Tsjerk Wassenaar"
> *An:* "Discussion list for GROMACS users"
> *Betreff:* Re: [gmx-users] Normal Mode Analysis
> Hi Stephen,
>
> You're confusing NMA with PCA.
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, Nov 26, 2013 at 6:30
Dear Gromacs users,
I am performing normal mode analysis (NMA) for a crystal, but
in the vibrational spectrum that obtained from NMA, there are no low
frequency lattice modes ( i.e., no peaks in spectrum below 50 cm-1). But
the spectrum that have obtained from velocity auto correl
On 3/17/15 8:16 AM, rahul dhakne wrote:
Dear all,
I am trying to perform the Normal Mode Analysis protein in water.
Here is the .mdp file I am using:
integrator = nm; time step
nsteps = 10 ; number of steps
nstlist
Dear All,
I am running simulations of a toxin placed in the middle of a bilayer. It
is known from the experiments that the equilibrium point of the toxin is in
one of the surfaces of the membrane.
I run MD with v-rescale a number of time-steps big enough to get the system
equilibrated with the tox
Dear Users,
I have encountered several questions when I try to perform NMA on a protein
structure from an equilibrated MD simulation. I were basically referred to
the gromacs manual (
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis) and some
threads in the mailing list.
First, G
hi ,
I've been trying to perform a nromal mode analysis using (after a thorough
energy minimization of my system)
prompt> mdrun_d -v -s nm.tpr -o nm.trr -mtx nm.mtx[...]
Maximum force: 8.56366e+00
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative
On 14/01/16 18:23, Mario Fernández Pendás wrote:
Dear All,
I am running simulations of a toxin placed in the middle of a bilayer. It
is known from the experiments that the equilibrium point of the toxin is in
one of the surfaces of the membrane.
What is an "equilibrium point"?
I run MD with v
Dear David,
Thank you very much for your answer.
2016-01-14 20:20 GMT+01:00 David van der Spoel :
> On 14/01/16 18:23, Mario Fernández Pendás wrote:
>
>> Dear All,
>>
>> I am running simulations of a toxin placed in the middle of a bilayer. It
>> is known from the experiments that the equilibriu
Den 2018-03-08 kl. 00:53, skrev Kevin C Chan:
Dear Users,
I have encountered several questions when I try to perform NMA on a protein
structure from an equilibrated MD simulation. I were basically referred to
the gromacs manual (
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis)
Thank you David for your reply. In fact, I have already been using the
double precision version of Gromacs.
I will greatly appreciate it if other questions could also be covered.
Thanks,
Kevin
Den 2018-03-08 kl. 00:53, skrev Kevin C Chan:
> >* Dear Users, *> >* I have encountered several questi
Hello Everyone,
I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but
find little useful.
My Gromacs was installed in a Linux cluster.
Follows is my steps to do normal mode analysis:
• pdb2gmx -ignh -ff < forcefield > -f 1SHS mutated.pdb -o mut.gro -p
topol.top
• editconf
Hello Everyone,
I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but
find little useful.
My Gromacs was installed in a Linux cluster.
Follows is my steps to do normal mode analysis:
• pdb2gmx -ignh -ff < forcefield > -f -o mut.gro -p topol.top
• editconf -f mut.gro
Why are you using PME-switch? Without explicitly choosing a switch?
Mark
On Thu, Dec 12, 2013 at 6:45 PM, mcfc1301 wrote:
> Hello Everyone,
>
> I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot
> but
> find little useful.
> My Gromacs was installed in a Linux cluster.
>
Hi all,
I am trying to do vibrational analysis for some high frequency modes in
peptides (using force field method), such as the N-H stretching, C=O
stretching, N-H bending, etc.
However, I got some unreasonable large frequencies, 6,000-250,000
wavenumbers, which are obviously not correct.
Hi all
I am trying to do a Normal Mode Analysis on a protein assembly with 1.05
million atoms
without solvent or ions. I ma trying to do so using Gromacs 5.0.4 double
precision
using 1024 processor and up to 256 GB of RAM, but it always fails.
I do not get any error message from Gromacs in j
can you give me more details? Is there any negative frequency you have
found?
On Fri, Jan 17, 2014 at 7:56 AM, Hao Ren wrote:
> Hi all,
>
> I am trying to do vibrational analysis for some high frequency modes in
> peptides (using force field method), such as the N-H stretching, C=O
> stretching
Dear All,
I am trying to find the full normal mode frequency spectrum of a small
protein. My system is composed of ~1900 atoms total, of which 130 are
protein atoms and the rest are solvent atoms. Since the Hessian matrix is
3Nx3N, the full spectrum for my system consists of ~5700 eigenfrequencies
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