Dear GMX user
I am working on enzyme ligand complex and want to calculate pmf of the complex.
I have successfully energy minimized and equilibrated the system.
But when I pull the ligand from the complex using the md_pull.mdp file then
instead of ligand the protein is come out of the system.
I ha
Hi ALL,
I am trying to simulate a protein inserted in a lipid bilayer with water and
ions, the entire system built using CG (coarse grain). I am using the
Martini force field to the CGMD simulation. My question is that should I use
the "centre of mass removal" component in my .mdp file (which we d
> Date: Thu, 12 Aug 2010 17:33:09 -0400
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Units of k1 in the pulling code
>
> Dear Xueming:
>
> the word "mol" is short form for "mole"
>
> http://en.wikipedia.org/wiki/Mole_%28unit%29
>
> In the pull code conte
Dear Chris
Thanks but I am not using periodic boundary conditions as I want to
simulate the two molecules in a vacuum.
Gavin
chris.ne...@utoronto.ca wrote:
> Dear Gavin:
>
> plot the position vs. time. Probably you will see it sample around one
> value, then discover a new state, and make a sha
On Aug 13, 2010, at 10:00 AM, Anirban Ghosh wrote:
Hi ALL,
I am trying to simulate a protein inserted in a lipid bilayer with
water and ions, the entire system built using CG (coarse grain). I
am using the Martini force field to the CGMD simulation. My question
is that should I use the "
Thanks a lot XAvier. And if one wants to study the self assembly of a GPCR
using CGMD (like you did for rhodopsin), should he/she use the same
parameters for COM motion removal?
Regards,
Anirban
On Fri, Aug 13, 2010 at 3:18 PM, XAvier Periole wrote:
>
> On Aug 13, 2010, at 10:00 AM, Anirban G
On Aug 13, 2010, at 12:37 PM, Anirban Ghosh wrote:
Thanks a lot XAvier. And if one wants to study the self assembly of
a GPCR using CGMD (like you did for rhodopsin), should he/she use
the same parameters for COM motion removal?
I guess so :))
Regards,
Anirban
On Fri, Aug 13, 2010 at 3
abdul wadood wrote:
Dear GMX user
I am working on enzyme ligand complex and want to calculate pmf of the
complex.
I have successfully energy minimized and equilibrated the system.
But when I pull the ligand from the complex using the md_pull.mdp file
then instead of ligand the protein is com
Jorge Alberto Jover Galtier wrote:
Hi, Justin.
Thank you for answering so quickly. We write you directly because we
receive the daily digest from Gromacs and we are not sure how to answer
to the thread. We have tried what you suggested, using 10,000 steps and
Reply to the message, strip o
Hi,
The problem just like this, in md.log
There are: 130889 Atoms
splitting topology...
Walking down the molecule graph to make constraint-blocks
There are 43925 charge gro
#ZHAO LINA# wrote:
Hi,
The problem just like this, in md.log
There are: 130889 Atoms
splitting topology...
Walking down the molecule graph to make constraint-blocks
The
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, August 13, 2010 7:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the mdrun choked or maybe braked.
#ZHA
#ZHAO LINA# wrote:
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, August 13, 2010 7:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the mdrun choked
Hi evergyone,
I analysed the number of hydrogenation bond with Gromacs 4.0.4 by running
g_hbond -s md.tpr -f md.xtc -num numhbond.xvg
There are 3 columns in the output files.
The first column = frame
The second column = H bonds
The third column = pairs within 0.35nm
The third colu
Jinyao Wang wrote:
Hi evergyone,
I analysed the number of hydrogenation bond with Gromacs 4.0.4 by running
g_hbond -s md.tpr -f md.xtc -num numhbond.xvg
There are 3 columns in the output files.
The first column = frame
The second column = H bonds
The third column = pairs within 0.
Hello,
Does gromacs write the current values (at some requested step) to
ENER.EDR or the averaged ones (at the requested interval)?
--
Dr. Vitaly Chaban
Associate Researcher
Department of Chemistry
University of Roshester, Rochester, NY 14642
--
gmx-users mailing listgmx-users@gromacs.org
h
Hello,
I'd like to ask a question about the conversion of the results of minimization
to pdb format. Here is what I do:
Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p
-o)Run editconf to define the box (editconf -d 1)run gromp and mdrun for the
minimizationRun e
The .edr file contains the instantaneous energies at every nstenergy steps.
-- original message --
Hello,
Does gromacs write the current values (at some requested step) to
ENER.EDR or the averaged ones (at the requested interval)?
--
gmx-users mailing listgmx-users@gromacs.org
http://list
abdullah ahmed wrote:
Hello,
I'd like to ask a question about the conversion of the results of
minimization to pdb format. Here is what I do:
1. Apply pdb2gmx to the pdb file to convert it to .gro and .top
(pdb2gmx -f -p -o)
2. Run editconf to define the box (editconf -d 1)
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Aug 13, 2010 at 8:08 AM, Justin A. Lemkul wrote:
>
>
> abdullah ahmed wrote:
>
>> Hello,
>>
>> I'd like to ask a question about the conversion of the results of
>> minimization to pdb format. Here is what I do:
>>
>> 1. Apply pdb2gmx to the p
To be more precise, it writes both the current values and the sum over the steps
to let g_energy print exact averages.
Berk
> Date: Fri, 13 Aug 2010 11:08:24 -0400
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] ener.edr
>
> The .edr file contains the instanta
Dear Chris
In relation to the correspondence below, I should've mentioned that the
peaks are symmetrical about the equilibrium distance as supposed to the
there being one main peak at the equilibrium distance. Also
should there be much of difference if you set pull_init to equal the
distance betwe
Berk, if I need the average values between 0...N, N...2N, etc - what
is the convenient way to get them automatically (in energy.xvg)?
Thank you,
Vitaly
>To be more precise, it writes both the current values and >the sum over the
>steps
>to let g_energy print exact averages.
--
gmx-users mailin
As I said before, please plot the position vs. time. It would be best
if you can make a graph of this and post it to some web tool. I use
photobucket, but there are many others.
I realize that you think you are starting at equilibrium, but there
are always things that can have unexpected co
In version 4.0 g_energy -aver prints the sum up till time t.
You then have to subtract the value at the previous step and divide
by the number of steps between frames.
You can also download 4.5-beta, there g_energy -aver will
directly print the averages over the last -nstenergy steps,
also of edr
Thanks Chris
I have equilibrated the system at 600 K in a previous run therefore
would it not be equilibrated, and also would the velocities from the
final configuration of the equilibration not be sufficient as
equilibrium velocities going into the main simulation
Gavin
chris.ne...@utoronto.ca
Gavin, I wish you the best of luck. Perhaps somebody else on the list
can help you.
-- original message --
Thanks Chris
I have equilibrated the system at 600 K in a previous run therefore
would it not be equilibrated, and also would the velocities from the
final configuration of the equilibra
Chris
Cheers and thanks for the suggestions.
P.S. I hope you don't think that the previous msg was in anyway rude. It
was actually a genuine question :)
Cheers
GAvin
chris.ne...@utoronto.ca wrote:
> Gavin, I wish you the best of luck. Perhaps somebody else on the list
> can help you.
>
> -- or
Also, is anybody aware of what the following option of g_energy performs:
-[no]averbool yes Print also the X1,t and sigma1,t, only if
only 1 energy is requested
If I compare the results of 'g_energy' and 'g_energy -aver', the
numbers are the same. Does it mean that g_energy print the av
Hi all.
I am trying to perform a tpi (test particle insertion) calculation on a
trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a Beowulf
cluster of Intel(R) Core(TM)2 Quad CPUQ6600 @ 2.40GHz). I am using
tpi integrator in the mdp file and the following command:
$ grompp -f
On 12/08/10 15:25, Alexandre Suman de Araujo wrote:
I'm simulating a system composed by a protein centered in a sphere of
water in vacuum.
The water molecules are kept within a virtual sphere with position
restrains between oxygen atom and a dummy atom fixed at the center of
the sphere. The prot
Em 13-08-2010 14:24, ms escreveu:
On 12/08/10 15:25, Alexandre Suman de Araujo wrote:
I'm simulating a system composed by a protein centered in a sphere of
water in vacuum.
The water molecules are kept within a virtual sphere with position
restrains between oxygen atom and a dummy atom fixed a
I have done PCA using first g_covar and got eigval.xvg and eigenvec.trr
files. The eigenvectors were analyzed by g_anaeig program and got
eigcomp.xvg, eigrmsf.xvg, proj.xvg, and 2dproj.xvg files. Then I want to
know
1. Which file among these shows relative positional fluctuation with
eigenvector in
On 13/08/10 18:30, Alexandre Suman de Araujo wrote:
I am just curious but... why are you doing actually all of this
instead of using a normal periodic solvent box?
The idea is to have less water molecules and, consequently, faster
simulations.
I thought about that, but I guessed you can use
Hi,
We discussed this a bit off-list, and just figured it would be good to include
the conclusions here too so people find it if they search the archives.
First, we definitely support all improper torsions of periodic form, such as
those in amber, charmm, and opls in OpenMM too, while Gromos us
Hi Gmx users,
I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna
check if the Volume is constant after the simulation.
I tried g_energy but did not find "Volume" in the pool of the options. Can
anyone help me?
Thanks,
Juju
--
gmx-users mailing listgmx-u
Rama G wrote:
Hi Gmx users,
I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I
wanna check if the Volume is constant after the simulation.
I tried g_energy but did not find "Volume" in the pool of the options.
Can anyone help me?
Box-X, -Y, and -Z are in the .edr file.
On Fri, 13 Aug 2010 18:23:40 -0400
"Justin A. Lemkul" wrote:
> Rama G wrote:
> > Hi Gmx users,
> >
> > I am using 4.0.X version of Gromacs and doing a NVT simulation. Now
> > I wanna check if the Volume is constant after the simulation.
> > I tried g_energy but did not find "Volume" in the pool o
Jussi Lehtola wrote:
On Fri, 13 Aug 2010 18:23:40 -0400
"Justin A. Lemkul" wrote:
Rama G wrote:
Hi Gmx users,
I am using 4.0.X version of Gromacs and doing a NVT simulation. Now
I wanna check if the Volume is constant after the simulation.
I tried g_energy but did not find "Volume" in the p
Thanks Justin,
but I did not find them, what I found are Vir-XY, YZ, XX,
Are these the same as Box-X, Y, Z, or perhaps can be converted to?
Btw, I am using 4.0.7 version.
One more Q', I saw your great gromacs tutor...@vt, but I am kinda confused you
used both NPT and NVT in position restrain
Thanks guys,
Sorry, I did not find "Density" in version 4.0.7. nor Box-X, Y, Z.
Any other way out?
Best,
Juju
From: Jussi Lehtola
To: gmx-users@gromacs.org
Sent: Fri, August 13, 2010 3:29:56 PM
Subject: Re: [gmx-users] Check V for NVT
On Fri, 13 Aug 2010
When you run an NVT simulation the box coordinates are not written out in
the edr file. You can try to extract the box information from your
trajectory files.
On Fri, Aug 13, 2010 at 6:42 PM, Rama G wrote:
>
> Thanks guys,
>
> Sorry, I did not find "Density" in version 4.0.7. nor Box-X, Y, Z.
>
Rama G wrote:
Thanks Justin,
but I did not find them, what I found are Vir-XY, YZ, XX,
Are these the same as Box-X, Y, Z, or perhaps can be converted to?
Btw, I am using 4.0.7 version.
See the latest post in the thread. The Vir-* terms refer to virial, which is
unrelated.
One more Q
Rama G wrote:
Thanks guys,
Sorry, I did not find "Density" in version 4.0.7. nor Box-X, Y, Z.
Any other way out?
The very absence of these terms indicates that your volume was constant. What
purpose do you have for checking it? Do you think something went wrong? If a
simple NVT didn't
Your language was not rude, but I did get frustrated after twice
asking you to perform an analysis and twice being ignored. My advice
still stands: plot the deviation vs. time and report back to the list.
Chris.
-- original message --
Cheers and thanks for the suggestions.
P.S. I hope you
- Original Message -
From: abdullah ahmed
Date: Saturday, August 14, 2010 1:05
Subject: [gmx-users] editconf
To: gmx
---
|
>
Hello,
>
> I'd like to ask a question about the conversion of the results of
> minimization to pdb for
Hi
To Calculate the radii of gyration about the principal axes
I use the command
g_gyrate -p
For lysozyme , I got =>
0.922754 1.22249 1.25603
but in some paper, the authors got
=> 0.660 0.833 0.991
It is a quite difference.
what is the definition of the radii of gyration about the
Hi All,
I am trying to build gromacs-4.0.7 on my gentoo box. My non-parallel
version of mdrun is working without any issues but when I try to run
the parallel version of mdrun, it kind of hangs (even no help info).
Some details-
1) $uname -a
Linux bingo 2.6.34-gentoo-r1 #7 SMP Fri Aug 13 10:18:23
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