hi GMX users
i have simulated the protein-ligand complex by gromacs for 20ns.
The average for the final structure of 18 to 20 nanoseconds has been
achieved.is minimization for the final average structure required?Sincerely.
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The 6-core Intel CPUs have only 28 PCI-E lanes rather than 40 like the
5830K/5860X which means that with a second GPU you'll get x16/x8 and
with three GPUs x8/x8/x8.
Also note that for the current GROMACS implementation, pairing a 5820K
with two 980s will likely give a rather imbalanced hardware s
Hi,
This all sounds super interesting. However, is there anything I can do for now
or do I need to just find the best combination by hand?
Thank you very much,
Max
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist
Hello gromacs users.
I am running GROMACS Tutorial of KALP15 in DPPC.
I am in the step define box and solvate.
after the command
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
i am getting an error as
Use of uninitialized value $box_x in multiplication (*)
On 9/30/14 5:51 AM, Anurag Dobhal wrote:
Hello gromacs users.
I am running GROMACS Tutorial of KALP15 in DPPC.
I am in the step define box and solvate.
after the command
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
i am getting an error as
Use of uni
On 9/30/14 3:36 AM, Mahboobeh Eslami wrote:
hi GMX users
i have simulated the protein-ligand complex by gromacs for 20ns.
The average for the final structure of 18 to 20 nanoseconds has been
achieved.is minimization for the final average structure required?Sincerely.
An average structure mi
Hi Max,
On 30 Sep 2014, at 09:40, Ebert Maximilian wrote:
> Hi,
>
> This all sounds super interesting. However, is there anything I can do for
> now or do I need to just find the best combination by hand?
For now you can add the “-npme all -min 0.25 -max 0.33” options to g_tune_pme
to make
it
Thank you Justin for your reply
as per your suggestion i verified the contents in confout.gro but i was
unable to check file as when i am clicking on it to open it I am getting an
message that file is of unknown type.
I again repeated the tutorial and I am getting the same things.
Thank you agai
On 9/30/14 7:06 AM, Anurag Dobhal wrote:
Thank you Justin for your reply
as per your suggestion i verified the contents in confout.gro but i was
unable to check file as when i am clicking on it to open it I am getting an
message that file is of unknown type.
A .gro file is not simply someth
Indeed, it is unlikely that averaged coordinates of certain structure
versus time correspond to something physically meaningful.
How do you average them, by the way? And what for, please?
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Tue, Sep 30, 2014 at 12:47 PM, Justin Lemkul wrote:
>
>
Dear users,
How can we define potassium ion in GROMOS ions.itp file?
Best,
H.A
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On 9/30/14 8:32 AM, h.aliza...@znu.ac.ir wrote:
Dear users,
How can we define potassium ion in GROMOS ions.itp file?
Exactly like the other ions. If there are suitable K parameters, define the
[moleculetype] and add the nonbonded parameters for the new atom type in
ffnonbonded.itp.
-Just
dear Justin thanks for your replyThe plot of the RMSD against time for the
trajectory generated with g_rms shows a maximum RMSD about 0.195 nm.
I set cut-off value to 0.2 nm for g_clusters command.
Is it a appropriate value?Sincerely.On Tuesday, September 30, 2014 2:17 PM,
Justin Lemkul wrote:
Hello everyone!
I tried to install Gromacs 5.0.1.
After this command:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
(as described in the gromacs installation information)
It tries to download of the regressiontest pack from the internet which is
no longer available.
I tried to t
Dear justin
Thank you for your rely and precious time.
I am aware that .gro file is to be visualized in VMD and its content can be
checked in text editor.
all the previous .gro file are visualized and checked in VMD.
I have obetained that ( confout.gro )file by running the command of energy
mini
On 9/30/14 10:30 AM, Anurag Dobhal wrote:
Dear justin
Thank you for your rely and precious time.
I am aware that .gro file is to be visualized in VMD and its content can be
checked in text editor.
all the previous .gro file are visualized and checked in VMD.
I have obetained that ( confout.g
On 9/30/14 9:58 AM, Mahboobeh Eslami wrote:
dear Justin
thanks for your reply
The plot of the RMSD against time for the trajectory generated with g_rms shows
a maximum RMSD about 0.195 nm.
I set cut-off value to 0.2 nm for g_clusters command.
Is it a appropriate value?
g_rms and g_cluster do
What works for me was to delete everything in the build directory before
re-running cmake. Give it a try and see if that helps.
--Farid
30.09.2014, 22:16, "Claudia Fernandes" :
> Hello everyone!
> I tried to install Gromacs 5.0.1.
>
> After this command:
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DR
Hi,
Spelling download with only one 'a' could help :-)
Mark
On Tue, Sep 30, 2014 at 4:16 PM, Claudia Fernandes <
cs.fernandes0...@gmail.com> wrote:
> Hello everyone!
> I tried to install Gromacs 5.0.1.
>
> After this command:
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>
>
Dear Gromacs users,
Is there any tutorial to simulate a protein in water solution containing
neutral zwitterionic osmolite such as trimethylglycine? Evaluating effects of
the compound on protein stability/secondary structure flexibility is to be
considered.
Regards,
Niyaz
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Gromacs Users mail
On 9/30/14 3:31 PM, niyaz.sabir wrote:
Dear Gromacs users,
Is there any tutorial to simulate a protein in water solution containing
neutral zwitterionic osmolite such as trimethylglycine? Evaluating effects of
the compound on protein stability/secondary structure flexibility is to be
conside
Hello, Justin,
you are always so helpful,
Regards,
NS
- Original Message -
From: "Justin Lemkul"
To: ; "niyaz.sabir"
Sent: Wednesday, October 01, 2014 12:33 AM
Subject: Re: [gmx-users] watrebox with osmolites
On 9/30/14 3:31 PM, niyaz.sabir wrote:
Dear Gromacs users,
Is ther
Unfortunately this is an ill-balanced hardware setup (for GROMACS), so
what you see is not unexpected.
There are a couple of things you can try, but don't expect more than a
few % improvement:
- try to lower nstlist (unless you already get a close to 0 buffer);
this will decrease the non-bonded ti
Dear all users,
I'm a newbie in MD. I would like to simulate a protein folding, from a
primary protein structure to a fully-folded state for a wild type and
mutated protein. Then I will compare them and make movie from unfolded to
folded state. I want to use REMD method. I want to know the system
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