hi all,
i would like to apply PCA (principal component analysis) for my peptides
that i simulated. i do know PCA for one trajectory but what if i have more
than one peptide ? how can i apply pca for example 10 peptides in a box ?
typically, i start with a PCA on the simulation
g_covar -s protein
hello:
I found with the default parameters of cmake, we can only get the single
precision gromacs 4.6. I am wondering how can we compile the double
precision?
thank you very much
best
Albert
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gmx-users mailing listgmx-users@gromacs.org
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hello:
I've got a qeustion the CPU for replica exchange. it said the REMD
should be performed by command:
mpiexec -x -np 8 mdrun -s sd_.tpr -multi 8 -preplex 1000
the above command have 8 different temperature and it specify 8 cores.
Does it mean the mdrun will use 1 core (8 in all) for eac
The TOTAL number of cores is specified by -np option. So it's 8 in all. By
the way, you can submit the job to see how. It'd be faster than waiting on
the list.
Terry
On Thu, Oct 18, 2012 at 3:20 PM, Albert wrote:
> hello:
> I've got a qeustion the CPU for replica exchange. it said the REMD
>
http://www.gromacs.org/Documentation/Installation_Instructions/Cmake#double_precision_build
Terry
On Thu, Oct 18, 2012 at 3:07 PM, Albert wrote:
> hello:
>
> I found with the default parameters of cmake, we can only get the single
> precision gromacs 4.6. I am wondering how can we compile the
Hi Tuba,
You can concatenate the trajectories with trjcat and perform PCA on
the resulting trajectory.
Cheers,
Tsjerk
On Thu, Oct 18, 2012 at 9:07 AM, Tuba Kilinc wrote:
> hi all,
>
> i would like to apply PCA (principal component analysis) for my peptides
> that i simulated. i do know PCA for
Hi everybody,
I have a question about the minimization of my protein. For this
minimization I fixed the backbone and the membrane atoms which around my
protein.
I minimized it 3 steps long but after step 20385 it stops with the
output:
Steepest Descents converged to machine precision in 2038
Hi Eva,
The change in energy in every step became smaller than the machine precision
can represent (as is stated in the output). In other words: your system is
minimized to a very high degree.
A value of 10 for the Fmax is very low for a system like yours, even with a
pure protein in water syst
On Thu, Oct 18, 2012 at 10:53 AM,
wrote:
> Steepest Descents converged to machine precision in 20385 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy = -8.8805600e+05
> Maximum force = 3.2341940e+02 on atom 3050
> Norm of force = 2.0930219e+00
>
> I do not see why
Hi Felix,
thank you for your answer.
So you think that a force of 3.2341940e+02 is okey? To work on?
I also tried to work on with a NVT run but then I got many many LINCS
warnings:
Step 1114, time 2.228 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000169, max 0.001796 (bet
It could be due to your mdp-settings. What's your time step? Do you use
constraints and virtual interaction sites?
Erik
18 okt 2012 kl. 12.04 skrev reising...@rostlab.informatik.tu-muenchen.de:
> Hi Felix,
> thank you for your answer.
> So you think that a force of 3.2341940e+02 is okey? To wor
18 okt 2012 kl. 12.08 skrev Ali Alizadeh:
> Dear All users
>
> 1- I have a symmetric simulation box but i can not produce a symmetric
> number density result (number density vs. z direction(nm))
>
> My simulation box is orthorhombic. My boundary condition is pbc but i
> don't perform any comman
Hi Erik,
my .mdp file looks like this:
define = -DPOSRES
integrator = steep
emtol = 10
nsteps = 3
nstenergy = 1
energygrps = System
coulombtype = PME
rcoulomb= 0.9
rvdw
On 10/18/12 6:15 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Erik,
my .mdp file looks like this:
define = -DPOSRES
integrator = steep
emtol = 10
nsteps = 3
nstenergy = 1
energygrps =
On 10/18/12 6:15 AM, Erik Marklund wrote:
18 okt 2012 kl. 12.08 skrev Ali Alizadeh:
Dear All users
1- I have a symmetric simulation box but i can not produce a symmetric
number density result (number density vs. z direction(nm))
My simulation box is orthorhombic. My boundary condition is p
On 10/18/12 5:26 AM, Arman M. Soufiani wrote:
Dear Friends,
I am simulating a protein-polymer interactive system.
I faced two problems.
First, when I added the ions to my solvated system, the polymer structure
shifted a little bit out of the PBC box. I really have no idea why this
happened!
Dear Justin
Please check my commands, Are these correct, step by step?
If these are correct then i will start my simulation with longer time,
1- pdb2gmx -f mixture.pdb -o mix -p mix
2- editconf -f mix.gro -o mix2.pdb ; for obtain a clean .pdb for
obtaining clean .gro and clean .top
3- pdb2
On 10/18/12 6:45 AM, Ali Alizadeh wrote:
Dear Justin
Please check my commands, Are these correct, step by step?
If these are correct then i will start my simulation with longer time,
I really don't understand why you're invoking pdb2gmx three times. You should
only ever need to produce
Hi Justin,
I already read the page you send me.
And I am sure about the first points. But I am not completely sure about
the mdp file for the nvt run.
It looks like this:
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 1
nstxout
This is not an NVT run. This is EM. Furthermore, I don't see the point in
combining position restraints with EM.
Erik
18 okt 2012 kl. 12.15 skrev reising...@rostlab.informatik.tu-muenchen.de:
> Hi Erik,
>
> my .mdp file looks like this:
>
> define = -DPOSRES
> integrator
On 10/18/12 7:08 AM, Ali Alizadeh wrote:
Dear Justin
On 10/18/12 6:45 AM, Ali Alizadeh wrote:
Dear Justin
Please check my commands, Are these correct, step by step?
If these are correct then i will start my simulation with longer time,
I really don't understand why you're invoking p
On 10/18/12 7:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
I already read the page you send me.
And I am sure about the first points. But I am not completely sure about
Sure about the first five points? The five suggestions on the page I linked are
all diagnostic s
Hi Erik,
this is my .mdp file:
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 1
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout= 0
nstenergy=
Hi Justin,
Well I already tried the protein without the membrane and I got the same
result. And I also make sure that I had no error messages during the
preparation runs.
I am using the amber03 force field.
My dummy atoms have a radius of 1.00 and a charge of 0.00. And yes they
are non bonded ato
On 10/18/12 8:51 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
Well I already tried the protein without the membrane and I got the same
result. And I also make sure that I had no error messages during the
preparation runs.
If the protein crashes in the absence of anythi
Hi Justin,
I am sorry, I switched the radius and the numbers:
radius=0
charge=1
mass=1
But I already tried it without the membrane and there I had the same
problem. And also when I did not restrained anything. Not even the
membrane I got the high force and the LINCS warnings.
Of what physical pro
Ah, so, right, you'll have to extract a trajectory for each peptide
and concatenate those trajectories.
Sorry for misreading...
Tsjerk
On Thu, Oct 18, 2012 at 9:44 AM, Tsjerk Wassenaar wrote:
> Hi Tuba,
>
> You can concatenate the trajectories with trjcat and perform PCA on
> the resulting traj
If you got the same problems with the protein only (and without any
restraints), I wonder if you have any non-standard residues (i.e. ligands or
protein modifications) present in your system?
Because a normal protein should work just fine with the parameters you gave us.
-Ursprüngliche Nachr
I have a cap "ACE" in the beginning of the protein but this was also
defined in the aminoacids.rtp file in the amber03 forcefield
> If you got the same problems with the protein only (and without any
> restraints), I wonder if you have any non-standard residues (i.e. ligands
> or protein modificat
Dear Justin Sorry for the inconvenience in the previous Mail .
I am Much obliged for your Previous help
Now I am following Your Lipid Protein Tutorial
I am using DPPC128.pdb And I Have Downloaded the DPPC.itp and topol_DPPC.top
When I run the energy Minimization (em.mdp Downloded form your w
On 10/18/12 11:21 AM, Ali Alizadeh wrote:
Dear All users
Average pressure(for my npt equilibration) could not reach my desired
value(300 bar desired , average value =279 bar)
Can i continue my npt equilibration in another npt equilibration for
reach my desired value?
Seems logical to me.
On 10/18/12 11:07 AM, vidhya sankar wrote:
Dear Justin Sorry for the inconvenience in the previous Mail .
I am Much obliged for your Previous help
Now I am following Your Lipid Protein Tutorial
I am using DPPC128.pdb And I Have Downloaded the DPPC.itp and topol_DPPC.top
When I run the en
Hi,
Did you try to plot the system pressure versus the simulation time to see if
you end up at ~ 300bar? I presume it will take some time to get this high
pressure and that would influence (i.e. lower) the average value.
Besides of that, I'm not sure how good barostats behave for such very high
Hello,
I am calculating the dipole moment auto-correlation function for my system
which have 128 cation and 128 anion.
I am saving the trajectory at each 2 ps and using this trajectory for
further analysis.
Can I save the dipole moment and three vectors at each 3 fs?
Thanks
Nilesh
--
gm
Dear Justin
Thank you for your reply,
Sincerely
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Dear all friends,
I wonder why we should impose POSRES on the protein in the system while
running NVT?! Shall we do so even for the system containing a short
peptide?!
What if I let the peptide, SOL+ions and my system's synthetic polymer apply
T-coupling individually?
I would be greatly thankful
Dear all friends,
I wonder why we should impose POSRES on the protein in the system while
running NVT?! Shall we do so even for the system containing a short
peptide?!
What if I let the peptide, SOL+ions and my system's synthetic polymer apply
T-coupling individually?
I would be greatly thankful
On 10/18/12 12:06 PM, Arman M. Soufiani wrote:
Dear all friends,
I wonder why we should impose POSRES on the protein in the system while
running NVT?! Shall we do so even for the system containing a short
peptide?!
Velocity generation causes atoms to move randomly, which can impart nasty for
Hi
The dipole is stored in the edr file, which output frequency is
controlled by "nstenergy" option in the mdp parameter file. Set it
appropriately during your run (nstenergy=0.003) but keep in mind that it
should be a multiple of the time step.
Javier
El 18/10/12 18:09, Nilesh Dhumal escr
On 10/18/12 1:45 PM, Javier Cerezo wrote:
Hi
The dipole is stored in the edr file, which output frequency is controlled by
"nstenergy" option in the mdp parameter file. Set it appropriately during your
run (nstenergy=0.003) but keep in mind that it should be a multiple of the time
step.
nst
On 2012-10-18 18:09, Nilesh Dhumal wrote:
Hello,
I am calculating the dipole moment auto-correlation function for my system
which have 128 cation and 128 anion.
I am saving the trajectory at each 2 ps and using this trajectory for
further analysis.
Can I save the dipole moment and three vector
In short, I can save dipole moment with the same frequency, the
trajectory save.
Nilesh
>
> On 10/18/12 1:45 PM, Javier Cerezo wrote:
>> Hi
>>
>> The dipole is stored in the edr file, which output frequency is
>> controlled by
>> "nstenergy" option in the mdp parameter file. Set it appropriate
In short, I can not save dipole moment directly. I can calculate dipole
moment only using .trr file.
Nilesh
>
> On 10/18/12 1:45 PM, Javier Cerezo wrote:
>> Hi
>>
>> The dipole is stored in the edr file, which output frequency is
>> controlled by
>> "nstenergy" option in the mdp parameter file. Se
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes that
are not standard cubes. I'm trying to run a membrane simulation where
a cyclic undecapeptide is inserted into the membrane and I want the
water layer to be sufficiently thick that if it were pulled, the
On 10/18/12 2:43 PM, klexa wrote:
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes that are not
standard cubes. I'm trying to run a membrane simulation where a cyclic
undecapeptide is inserted into the membrane and I want the water layer to be
sufficiently thi
On 10/18/2012 11:53 AM, Justin Lemkul wrote:
On 10/18/12 2:43 PM, klexa wrote:
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes
that are not
standard cubes. I'm trying to run a membrane simulation where a cyclic
undecapeptide is inserted into the membrane
On 10/18/12 3:04 PM, klexa wrote:
On 10/18/2012 11:53 AM, Justin Lemkul wrote:
On 10/18/12 2:43 PM, klexa wrote:
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes that are not
standard cubes. I'm trying to run a membrane simulation where a cyclic
undecapept
Hi All
Is it possible to have to fix the temperature of one subsystem, but leave the
other parts alone?
Say for example you have protein and solvent, so what would happen if you only
have a single
tc_grps = SOL
and leave Protein alone.
Reason I ask is I would like to look at the time depende
On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote:
>
>
> On 10/18/12 2:43 PM, klexa wrote:
> > Hi Gromacs users,
> >
> > I think I am a bit confused about the proper way to handle boxes that are
> > not
> > standard cubes. I'm trying to run a membrane simulation where a cyclic
> > undecapeptid
On 10/18/12 3:55 PM, Peter C. Lai wrote:
On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote:
On 10/18/12 2:43 PM, klexa wrote:
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes that are not
standard cubes. I'm trying to run a membrane simulation where a cy
On 2012-10-18 03:58:22PM -0400, Justin Lemkul wrote:
>
>
> On 10/18/12 3:55 PM, Peter C. Lai wrote:
> > On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote:
> >>
> >>
> >> On 10/18/12 2:43 PM, klexa wrote:
> >>> Hi Gromacs users,
> >>>
> >>> I think I am a bit confused about the proper way to han
We published the half-epsilon double-pairlist method for combining opls-aa/l
proteins with Berger lipids in gromacs. An extension to amber protein and
berger lipids was subsequently published by another group after our suggestions
on this list. You can find my tips on how to extend the half-epsi
Justin is right. I've slipped a bit, that was not the way to set
nstenergy. But still, you can save the dipole directly in the edr file.
Not from your existing trajectory, but in a new run. Say your dt=1fs,
then you should set nstenergy=3 to get your dipole moment every 3fs
which you can retrie
How can I save the total dipole moment extacted by .edr file?
I could not find the option in g_energy.
Nilesh
> Justin is right. I've slipped a bit, that was not the way to set
> nstenergy. But still, you can save the dipole directly in the edr file.
> Not from your existing trajectory, but in
Hi, Gromacs users,
If you have time, I am wondering if you have any advice, as a favor.
I'm a graduate student in computational chemistry in the U.S. My department
has an EXCELLENT "in-house" cluster, on which I routinely run Gromacs jobs
on 8 to 24 cores. However, it occasionally happens that
Try 100 ns of simulation. Also, note that g_density will not generally give you
the correct result if you are using
pressure coupling. This is because g_density builds the histogram up from z=0
to z=max and if you center
your bilayer using pressure coupling then the center of the bilayer will n
On 10/18/12 8:14 PM, Ali Alizadeh wrote:
Dear All users
Dimension of my simulation box after nvt equilibration changed, Why?
My pressure for equilibration is = 300 bar
My simulation box was shrunk !!
You're applying a huge pressure to your system, and if your starting
configuration is no
Hi Andrew,
We at Rescale (www.rescale.com) provide this exact on-demand service
for running Gromacs jobs directly through your browser.
You can register at https://platform.rescale.com/register/, to get you
started we are happy to provide you with some free hours to get you up
and running. Our p
Is it possible to calcualte the dipole moment at 3fs by modifing the
source code?
Nilesh
> How can I save the total dipole moment extacted by .edr file?
>
> I could not find the option in g_energy.
>
> Nilesh
>
>
>> Justin is right. I've slipped a bit, that was not the way to set
>> nstenergy. B
hello:
I am trying to submit replica exchange jobs to cluster by following
command, but failed:
g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000
-reseed -1 -launch
Here is the log file:
---
Program g_tune_pme_d, VERSION 4
Hello,
Basically is telling you that the output (.tpr) file that grompp should
have created is not there to be read.
Check if grompp ran correctly and produced the wanted output. I suspect
that it may have failed for some reasons.
Hope this helps,
Cheers,
Davide
On 19/10/12 7:37 PM, "Albert"
hello David:
thanks for kind reply.
The .tpr file was created by grompp in cluster and there is no problem
for that.
thank you very much
Albert
On 10/19/2012 08:52 AM, Davide Mercadante wrote:
Hello,
Basically is telling you that the output (.tpr) file that grompp should
have created is not
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