Dear Gromacs users,
I'm thinking about purchasing a GPU workstation for some simulation work, and
was wondering about the optimal CPU-GPU combination for running MD as I'm
pretty clueless about the hardware side of things.
Typical systems simulated would be membrane protein systems of around 10
Dear GROMACS users,
I want to simulate DNA in a cubic box with water as solvent and visualize
it.
By using -pbc mol I can see part of the DNA is out of the box so I want to
center the DNA in box.
But using -center seems destruct the DNA into several parts. I tried to use
-pbc mol followed by -cente
Dear gmx users,
In an attempt to analyse the interaction between a Protein and a Bilayer (in a
CG MD simulations) i’m using gmx distance as following:
gmx distance -f DFMG-200ns.xtc -s DFMG-200ns.tpr -n index.ndx -select 'com of
group "Protein" plus com of group "Membranes"' -oall distance.xvg.
B
Thanks so much João, I will certainly try it.
On Tue, Jul 14, 2015 at 4:11 PM, João Henriques <
joao.henriques.32...@gmail.com> wrote:
> You're most welcome. By the way, I found this old thread where Justin
> suggests the same solution using the COM pulling:
>
> http://comments.gmane.org/gmane
You're most welcome. By the way, I found this old thread where Justin
suggests the same solution using the COM pulling:
http://comments.gmane.org/gmane.science.biology.gromacs.user/44479
This is probably your best option for "helping" the protein(s) to stay
inside the membrane. I would definitely
Dear João,
Thanks for the reply.
The solution structures of the peptide certainly wont stay in the membrane.
The purpose of the study is to see if my peptide will go transmembrane.
Specifically, it is a 21 amino acid peptide that could potentially adopt a
transmembrane configuration in an oligom
You can do something else if you don't want to use position restraints on
the protein. You can try the "COM pulling" options, which can be used to
constraint the center of mass (COM) of two or more groups in a simulation.
In this case, you could add one for the COM of the protein and that of the
me
Dear Shivangi,
To me - if I understood your problem correctly - there's no point in using
walls. Why don't you just use position restraints for the protein? When I
think of walls, I think of surface adsorption studies and such.
Furthermore, when you use walls in gromacs you're including an additio
Hi,
It looks like the the problem is the asymmetry in ion distribution. I have
seen from the literature that such ion asymmetry can be maintain by
implementing slab geometry. Can anybody provide me some information of how
to build vacuum slab above and below the membrane ( ie in Z direction).
Wha
Hello All,
Is there any tutorial/example of how to apply wall potential in GROMACS.
I basically want to design a system where there are two walls just above
and below the head groups of a bilayer, so that I am able to restrain an
inserted peptide from popping out to the surface or in water.
http
Dear Natalie,
Feel well!
If you'll have questions feel free to ask.
Best regards,
Asaf
Quoting Natalie Nguyen :
Dear Asaf,
I was ill this weekend but I a better now!
I will try to simulate the system as the way as you instructed and
will let you know my results!
Thank you again,
Natalie
Dear Asaf,
I was ill this weekend but I a better now!
I will try to simulate the system as the way as you instructed and will let you
know my results!
Thank you again,
Natalie
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of
asaffa
On 7/14/15 3:07 AM, Sun Iba wrote:
Hello Everyone
I am simulation a protein as per the lysozyme tutorial. MY simulation got
dumped at final mdrun step. It is showing following warning :
Command line:
gmx mdrun -deffnm md_0_1
Reading file md_0_1.tpr, VERSION 5.0.5 (single precision)
Using 1
Hi all,
I have a couple of quick questions. I am simulating DNA duplex with
some fullerene derivatives. The fullerenes are expected to accommodate
themselves in the major groove of the DNA and I am getting similar results.
However, the parallel DNA chains are getting deformed which is also
Hi,
It's a periodic box, right? There is only one water region. You can't get
steady-state non-equilibrium ion distribution without forcing it, e.g.
https://www.mpibpc.mpg.de/grubmueller/compel
Mark
On Tue, Jul 14, 2015 at 12:42 PM anu chandra wrote:
> Dear Gromacs users,
>
> I am working with
Dear Gromacs users,
I am working with membrane proteins. The system contains CaCl2 ions and I
build the system with calcium ions on one side of the membrane (here, upper
layer) and chloride ions distributed on both side of the membrane, in order
to maintain the physiological condition. Unfortunat
Hi,
Was that actually your mdrun command line? I think you need
gmx mdrun -s md_0_2 -deffnm md_0_1 -cpi md_0_1 (with or without -append)
to actually get appending happening. mdrun does not deduce the names of the
output files from the contents of the checkpoint file.
Mark
On Tue, Jul 14, 2015
Hi Mark,
in the .log file there are this lines at the start of the extending.
There are: 20587 Atoms
Charge group distribution at step 50: 5190 5166 5109 5122
Initial temperature: 319.123 K
Started mdrun on rank 0 Sun Jul 12 20:50:29 2015
Step Time Lambda
Hi,
On Tue, Jul 14, 2015 at 8:10 AM Andrea Spinelli
wrote:
> @Mark
> The .log report works for 2000 ps.
>
Sure, but you need to look at the bit between 1 ns and 2 ns to find out
what happened when you attempted to append.
Mark
> @Chaban
> I not use grompp and the extension not create .trr fi
Hello Everyone
I am simulation a protein as per the lysozyme tutorial. MY simulation got
dumped at final mdrun step. It is showing following warning :
Command line:
gmx mdrun -deffnm md_0_1
Reading file md_0_1.tpr, VERSION 5.0.5 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads
start
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