Dear all,
I have reported a week ago update about my troubles with octanol/water slab
and pulling simulations, where COM code starts to report a wrong distances
between centre-of-masses between two groups when bigger box (see bellow) is
used.
So far, smaller box cured our actual calculation
Dear All
I use the g_clustersize to examine the cluster decay vs. time during the
aggregation process of glycolipids into a micelle with the following
command:
$WORKDIR/gromacs-4.5.3/bin/g_clustsize_mpi -f *.xtc -s run_1.tpr -mc
bDM-AMBER99SB-ILDN-Self_b_cluster.xvg -nc
Hi,
I would suggest you extract the single snapshot from your xtc file and
then run the analysis tool on the single snapshot file.
/Flo
On Tue, 2011-09-06 at 12:12 +0200, intra\sa175950 wrote:
Dear All
I use the g_clustersize to examine the cluster decay vs. time during
the
Dear gmx users,
Are there some tutorials on constant PH simulations using gromacs? How should I
state my work? Right now I have no idea on it.
--
Best wishes,
Qinghua Liao
Ph.D student of Tianjin University, China--
gmx-users mailing listgmx-users@gromacs.org
fancy2012 wrote:
Dear gmx users,
Are there some tutorials on constant PH simulations using gromacs? How
should I state my work? Right now I have no idea on it.
Interestingly enough, there is a page devoted to this topic on the Gromacs wiki:
Look for the pKa-constants of each part of your system (e.g. each amino-acid).
Then you can check each protonation state and change it according to your
application in the force-field.
Emanuel
fancy2012 06.09.11 13.01 Uhr
Dear gmx users,
Are there some tutorials on constant PH simulations
Dear All,
I’m a new NAMD user and use NAMD and
VMD for simulations. I want to ask a question about trajectory analysis. I
examined the gromacs 4.5.4 tools for making analysis and decided to use some of
them for my NAMD output files. Is there a way to convert my namd output files
into gromacs
Namd Namd wrote:
Dear All,
I’m a new NAMD user and use NAMD and VMD for simulations. I want to ask
a question about trajectory analysis. I examined the gromacs 4.5.4 tools
for making analysis and decided to use some of them for my NAMD output
files. Is there a way to convert my namd output
That is not considered constant-pH MD.
Follow Justin's suggestion.
Cheers,
João
On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter
emanuel.pe...@chemie.uni-regensburg.de wrote:
Look for the pKa-constants of each part of your system (e.g. each
amino-acid).
Then you can check each protonation
Are you 100% sure that you have the correct index group for your large
box? Did you use a .ndx file that you prepared as input to mdrun or
did you rely on the creation of a standard group? If you relied on the
creation of a standard group, can you please try again with the larger
box and a
On 6/09/2011 11:39 AM, Sweta Iyer wrote:
Hi all,
I have been trying to pdbgmx my protein to obtain the gro and top files as
follows:
pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top -ter -ignh
However, I get an error message that states:
Atom OXT in residue SER 29 was not found in rtp
Could you just tell me smth. !
No forcefield on whole earth is able to reproduce the pH realistically
by H+.
You just can apply pH of your system through the protonation states
of each part in your system.
monkey.
João M. Damas 06.09.11 14.22 Uhr
That is not considered constant-pH MD.
Emanuel Peter wrote:
Could you just tell me smth. !
No forcefield on whole earth is able to reproduce the pH realistically
by H+.
You just can apply pH of your system through the protonation states
of each part in your system.
Constant protonation state and constant pH are different.
As Justin said, constant protonation != constant pH.
Constant-pH MD does not simulate H+, but allows changes in protonation
states during the MD simulation. There are different algorithms
to accomplish that.
Cheers,
João
On Tue, Sep 6, 2011 at 2:04 PM, Emanuel Peter
Dear Gromacs Users,
I am calculating hbonds between my 10 ligands and each residue... How does
Gromacs calculate average number of hbonds per timeframe?
Example:
for Glycine:
Av. num of hbonds/timeframe
0.96
To check whether that is correct I added all hbonds formed with Glycine
during my
Namd Namd wrote:
Dear Justin,
Well , I think that I can do it , can't I ? I have gromacs 4.0.7 and VMD
1.8.7 . how can I make analysis using NAMD output files with these
You can't do it with 4.0.7, only the 4.5.x series has the capability to use VMD
libraries. Your first message said
Steven Neumann wrote:
Dear Gromacs Users,
I am calculating hbonds between my 10 ligands and each residue... How
does Gromacs calculate average number of hbonds per timeframe?
Example:
for Glycine:
Av. num of hbonds/timeframe
0.96
To check whether that is correct I added all hbonds
The standard procedure of H+ interchange and transition states can be done
through QM/MM.
Please give one reference according to the algorithms you have mentioned.
Cheers.
João M. Damas 06.09.11 15.19 Uhr
As Justin said, constant protonation != constant pH.
Constant-pH MD does not simulate
On 6/09/2011 11:37 PM, Steven Neumann wrote:
Dear Gromacs Users,
I am calculating hbonds between my 10 ligands and each residue... How
does Gromacs calculate average number of hbonds per timeframe?
Example:
for Glycine:
Av. num of hbonds/timeframe
0.96
To check whether that is correct I added
Emanuel Peter wrote:
The standard procedure of H+ interchange and transition states can be done
through QM/MM.
Please give one reference according to the algorithms you have mentioned.
There are several cited at:
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
-Justin
On Tue, Sep 6, 2011 at 2:50 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 6/09/2011 11:37 PM, Steven Neumann wrote:
Dear Gromacs Users,
I am calculating hbonds between my 10 ligands and each residue... How does
Gromacs calculate average number of hbonds per timeframe?
Example:
for
Steven Neumann wrote:
On Tue, Sep 6, 2011 at 2:50 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 6/09/2011 11:37 PM, Steven Neumann wrote:
Dear Gromacs Users,
I am calculating hbonds between my 10 ligands and each
residue...
On Tue, Sep 6, 2011 at 3:09 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Tue, Sep 6, 2011 at 2:50 PM, Mark Abraham mark.abra...@anu.edu.aumailto:
mark.abra...@anu.edu.**au mark.abra...@anu.edu.au wrote:
On 6/09/2011 11:37 PM, Steven Neumann wrote:
Steven Neumann wrote:
On Tue, Sep 6, 2011 at 3:09 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
On Tue, Sep 6, 2011 at 2:50 PM, Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au
Hi, all
I am learning GROMACS 4.5.1 recently and encountered a problem that puzzled
me for weeks. I am wondering if someone can help me with this.
Here is the problem: I was trying to perform a MD simulation for 216 ethane
molecules in a box. I have first generated a box of ethane with random
Phil (Yang) Song wrote:
Hi, all
I am learning GROMACS 4.5.1 recently and encountered a problem that
puzzled me for weeks. I am wondering if someone can help me with this.
Here is the problem: I was trying to perform a MD simulation for 216
ethane molecules in a box. I have first generated
On 7/09/2011 12:40 AM, Phil (Yang) Song wrote:
Hi, all
I am learning GROMACS 4.5.1 recently and encountered a problem that
puzzled me for weeks. I am wondering if someone can help me with this.
Here is the problem: I was trying to perform a MD simulation for 216
ethane molecules in a box. I
2. Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter)
Message: 2
Date: Tue, 06 Sep 2011 15:49:28 +0200
From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de
Subject: Antw: Re: Re: [gmx-users] constant PH simulations
To: gmx-users@gromacs.org
Message-ID:
No forcefield on whole earth is able to reproduce the pH realistically
by H+.
You just can apply pH of your system through the protonation states
of each part in your system.
I guess someone has been living in a cave for the past decade or so...
Cheers,
--
João Henriques
--
gmx-users mailing
Hi All,
I am trying to run simulations of a small protein with the backbone frozen,
but not the side chains. It looks like neither position restraint run or
defining freeze_group will work since these options will freeze atoms in
space. I also noticed that I may define [dihedral_restraints]
seunghwan lee wrote:
Hi All,
I am trying to run simulations of a small protein with the backbone frozen,
but not the side chains. It looks like neither position restraint run or
defining freeze_group will work since these options will freeze atoms in
space. I also noticed that I may define
Hi,
I am wondering when Gromacs will support OpenMM 3+ and my GPU
architecture (S2050C Teslas)? I have been patiently waiting, and
still haven't seen a new version (and yes, I have pulled back a
development version from git). Still getting this nonsensical error
from OpenMM2 and while OpenMM3
Hi all,
I used pdb2gmx and selected amber99sb for generation of itp files of a
normal peptide within GROMACS 4.5.4.
But I saw that all the bonds, angles, and dihedral parameters (c0, c1, c2
...) were not present in the itp file, while only funct is defined. It seems
the same thing happens with
Yun Shi wrote:
Hi all,
I used pdb2gmx and selected amber99sb for generation of itp files of a
normal peptide within GROMACS 4.5.4.
But I saw that all the bonds, angles, and dihedral parameters (c0, c1,
c2 ...) were not present in the itp file, while only funct is defined.
It seems the
Dear users,
I have a short question about temperature dependence of enregy terms i.e
bonds, angles, torsions, vdw , electorstatics. I am curious why these
energies increase with T. Especially bonded terms that have no temperature
dependence in the functional form ( force constants), why all
Juliette N. wrote:
Dear users,
I have a short question about temperature dependence of enregy terms i.e
bonds, angles, torsions, vdw , electorstatics. I am curious why these
energies increase with T. Especially bonded terms that have no
temperature dependence in the functional form ( force
Hi,
Thank everyone for your suggestions.
I have tried to put less molecule in a small box and find this works!
Eventually I have solve the problem by using a larger initial box size for
the random generated position and orientation. It seemed that the overall
interaction of OPLS-AA between
On 6 September 2011 15:03, Justin A. Lemkul jalem...@vt.edu wrote:
Juliette N. wrote:
Dear users,
I have a short question about temperature dependence of enregy terms i.e
bonds, angles, torsions, vdw , electorstatics. I am curious why these
energies increase with T. Especially bonded
Juliette N. wrote:
On 6 September 2011 15:03, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Juliette N. wrote:
Dear users,
I have a short question about temperature dependence of enregy
terms i.e bonds, angles, torsions, vdw ,
Hi All,
when I grompp for energy minimization, I met the error like,
--
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
processing topology...
Opening library file
Yao Yao wrote:
Hi All,
when I grompp for energy minimization, I met the error like,
--
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
processing topology...
Opening library file
Yao Yao wrote:
Hi Justin,
Thanks for your reply. Is there a way I can use explicit water to get
rid of the error?
Solvate as you would any normal system and don't try to use force field files
from newer versions.
-Justin
Thanks,
Yao
I mean if I still want to use the introduced amber03 ff, when I solvate it as
normal, it asks for gbsa.itp,
--
Fatal error:
Library file gbsa.itp not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
--
So
Yao Yao wrote:
I mean if I still want to use the introduced amber03 ff, when I solvate
it as normal, it asks for gbsa.itp,
--
Fatal error:
Library file gbsa.itp not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
Hello Juliette:
If you observe such behavior, I would suggest just to decrease a
time-step. You should have the same energies at all temperatures.
The larger is a time-step, the larger is a deviation from the energy
minimum (bonded potentials). The larger is the deviation, the higher
Dr. Vitaly V. Chaban wrote:
Hello Juliette:
If you observe such behavior, I would suggest just to decrease a
time-step. You should have the same energies at all temperatures.
The larger is a time-step, the larger is a deviation from the energy
minimum (bonded potentials). The larger is the
On 6 September 2011 15:42, Dr. Vitaly V. Chaban vvcha...@gmail.com wrote:
Hello Juliette:
If you observe such behavior, I would suggest just to decrease a
time-step. You should have the same energies at all temperatures.
The larger is a time-step, the larger is a deviation from the energy
Justin, I was speaking only about the bonded (and presumably,
harmonic) potentials. Decreasing the time-step, as I mentioned, never
made the things worse.
Vitaly
On Tue, Sep 6, 2011 at 7:59 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Dr. Vitaly V. Chaban wrote:
Hello Juliette:
If you
Dr. Vitaly V. Chaban wrote:
Justin, I was speaking only about the bonded (and presumably,
harmonic) potentials. Decreasing the time-step, as I mentioned, never
made the things worse.
How is it that harmonic potentials are unaffected by temperature? Thermal
excitation of bonds is a real
On 7/09/2011 3:53 AM, João Henriques wrote:
I guess someone has been living in a cave for the past decade or so...
Please keep contributions to the mailing list constructive :-)
Everyone's been wrong before!
Mark
--
gmx-users mailing listgmx-users@gromacs.org
On 7/09/2011 5:01 AM, Juliette N. wrote:
Dear users,
I have a short question about temperature dependence of enregy terms
i.e bonds, angles, torsions, vdw , electorstatics. I am curious why
these energies increase with T. Especially bonded terms that have no
temperature dependence in the
On 7/09/2011 5:23 AM, Phil (Yang) Song wrote:
Hi,
Thank everyone for your suggestions.
I have tried to put less molecule in a small box and find this works!
Eventually I have solve the problem by using a larger initial box size
for the random generated position and orientation. It seemed
Hello,
The last 6 months I've been working with gromacs (4.5.3 and 4.5.4) in Ubuntu
(10.4) and it has worked fine. The problem started when I changed the linux
distribution to Scientific Linux (5.3)... I followed the same steps to
download/configure gromacs but something's wrong or missing
Dear gmx-users,
I am pretty confused about how to calculate the surface tension of a bilayer
which with its bilayer
normal in y-direction rather than z-direction (as the default).
How does the Surf*SurfTen option in g-energy work? Does it take z as a
default bilayer normal?
If so, how can I
Dear gmx-users,
Could anyone help me with the calculation of 3D pressure profile in a
function of y?
I used the provided gromacs-4.0.2_localpressure for my calculatioin. It
calculate
the 3D pressure profile as a function of z (the default setting of bilayer
normal
is z-direction).
In my case, I
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