Thank you Szilárd,
So I would be really thankful if you could tell me which configuration is
the best:
2x GTX 980
2x GTX 780 Ti
2x GTX Titan Black
Sincerely,
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On Mon, Oct 20,
Hi,
On 27 Oct 2014, at 07:11, Mohammad Hossein Borghei mh.borg...@gmail.com wrote:
Thank you Szilárd,
So I would be really thankful if you could tell me which configuration is
the best:
2x GTX 980
2x GTX 780 Ti
2x GTX Titan Black
I would choose between the 980 and the 780Ti, which will
and how to use that 2 cores? i think that would increase performace twice
as now i am running 1 core per replica.
On Mon, Oct 27, 2014 at 7:15 AM, Justin Lemkul jalem...@vt.edu wrote:
On 10/26/14 9:55 AM, Nizar Masbukhin wrote:
regarding gaining speed in implicit solvent simulation, i have
Hi,
on the fly try this using ALA1 as example (it can be any of your residues):
`grep -v '^#\|^@' rama.xvg | grep ALA1 | awk '{if($2 == 0) print $2}'
| awk -f std.awk
where std.awk contains:
{
x1 += $1
x2 += $1*$1
}
END {
x1 = x1/NR
x2 = x2/NR
sigma = sqrt(x2 - x1*x1)
if (NR
replace with this:
`grep -v '^#\|^@' rama.xvg | grep ALA1 | awk '{print $2}' | awk -f
std.awk
On 27/10/2014 11:04, andrea wrote:
Hi,
on the fly try this using ALA1 as example (it can be any of your
residues):
`grep -v '^#\|^@' rama.xvg | grep ALA1 | awk '{if($2 == 0) print
$2}' | awk
On Sun, Oct 26, 2014 at 11:44 PM, Eric Smoll ericsm...@gmail.com wrote:
Hi Mark,
Thank you for responding so rapidly. I should note that identical
processing (I use a script) on the trajectories produced by slightly
different chemical systems had no problem and trajconv produced a complete
Hi Mark,
i understand. It wasn't getting stuck in one place, if I skip over the
problem time when executed from the beginning the slowdown still occurs.
I am working on the Stampede Supercomputer using their install of gromacs
and for reasons I do not understand, this extremely slow processing
On 10/27/14 1:25 AM, Seera Suryanarayana wrote:
Dear Gromacs Users
I would like to analyze frame number 150 to 160 out of 1000 frames. I have
been trying to load frames of my interest into vmd. But I was not able to
do it. Please tell me how to use it.
If you're having problems with VMD,
Hey :)
That should use circ.awk:
{
x1 += sin($1)
x2 += cos($1)
}
END {
m = atan2(x1,x2)
print Number of points = NR
print Circular Mean = m
}
Otherwise, the mean of 180 and -180 gives you a 0 angle.
Cheers,
Tsjerk
On Mon, Oct 27, 2014 at 11:11 AM, andrea andrea.spital...@iit.it
Hi,
Parallel file systems do give uneven service (e.g. one file has a chunk
that lives somewhere that was under high load right when you asked for
it...), so given that you can read the files normally on a normal
filesystem, then you should double-check Stampede's user guides for how to
make best
On Oct 27, 2014, at 3:14 AM, Carsten Kutzner wrote:
Hi,
On 27 Oct 2014, at 07:11, Mohammad Hossein Borghei
mh.borg...@gmail.commailto:mh.borg...@gmail.com wrote:
Thank you Szilárd,
So I would be really thankful if you could tell me which configuration is
the best:
2x GTX 980
2x GTX 780 Ti
Hi,
We use systems with 780 Ti , 12 cores and have had no problems running
Gromacs. Gives a performance of ~ 100 ns/day for a system with 35000 atoms.
Regards,
Abhishek
On Mon, Oct 27, 2014 at 7:05 PM, Adelman, Joshua Lev jl...@pitt.edu wrote:
On Oct 27, 2014, at 3:14 AM, Carsten Kutzner
Hi I used to find the link for searching the previous posted discussions and
all the threads in the gromacs home page where there used to be a 'search'
option for looking for discussions on a topic. But, now, looking for the same
archive in Mailing Lists - Gromacs redirects me to gromacs home
Dear all,
we are trying to simulate a vesicle in water using united-atoms
(Gromos96/ffG45a3). The system was modelled with the VesicleBuilder and
the MembraneEditor. So first the vesicle was built (with 3 components: 2
PC, 1 Chol), and then it was embedded in a water (spc216) box with
Dear Manuel/Björn,
you cannot ignore that vesicle-like structures have a complex interfacial
energy, with terms arising from both the packing of lipids and the
curvature of the interface, among other factors. If it happens that you
placed the wrong number of water molecules inside the cavity,
Hi Bjorn,
I agree with Andre. Pack more water molecules inside the vesicle than what
you currently have. It is likely that the water penetrates quite a bit into
the headgroups, and hence you need more waters than you think (since water
can hydrogen bond with the lipid head groups). Also try
On 10/27/14 11:07 AM, Sanku M wrote:
Hi I used to find the link for searching the previous posted discussions
and all the threads in the gromacs home page where there used to be a
'search' option for looking for discussions on a topic. But, now, looking for
the same archive in Mailing Lists
i dont really understand the point. could you please what do you mean in
the last reply?
what command should i use?
if, say i have 72 cores in 9 nodes, and 16 replicas to simulate in implicit
solvent.
On 10/27/14 5:59 AM, Nizar Masbukhin wrote:
and how to use that 2 cores? i think that would
Hello Bjorn
I don't know if it related to your problem, but I see a typo in our mdp file
for the pressure coupling:
Pcoupltype = isotropic ;semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 4.0 4.0
compressibility
Dear gmx-users
I built a graphene sheet (graphene.pdb ) by VMD. I convert it to gro file with
editconf command. Then I made top file with g_x2top command. But in top file
connection between atoms is not correct(highlighted lines below). How can I
solve this problem?
Connection in pdb file for
Dear Andre, Rajat Stephane,
thanks a lot for your light-speed suggestions!
@More Water Idea
I'll try to remove as less water as possible in my next try.
But, what bothers me is the fact, that I manually added some water after
the vacuum bubble was formed and equillibrated again, which
On Mon, Oct 27, 2014 at 6:05 PM, Nizar Masbukhin nizar.fku...@gmail.com
wrote:
i dont really understand the point. could you please what do you mean in
the last reply?
what command should i use?
if, say i have 72 cores in 9 nodes, and 16 replicas to simulate in implicit
solvent.
Hi,
You
Dear Bjorn,
A few thoughts:
1) Are you simulating a coarse grained system (Martini) or an all-atom
system. Isotropic pressure coupling may be more appropriate for a vesicle
because of its spherical symmetry.
2) When you manually added water, did you do it in the vacuum bubble region
only?
3) What
Dear Manuel/Björn,
based on your description, I guess that placing some more water after the
bubble has formed may not work as expected, because the bilayer forming the
vesicle might be somehow strained, that's why a suggested stepping back to
the system before equilibration. I think the number
Dear Users
In my .gro file the molecules section contains the following :-
[ molecules ]
; Compound#mols
DNA_chain_D 1
Protein_chain_L 1
Protein_chain_H 1
Now , I want to do a pulling simulation where , I want both chain L and
chain H to be pulled simultaneously as an
On 10/27/14 5:27 PM, Agnivo Gosai wrote:
Dear Users
In my .gro file the molecules section contains the following :-
[ molecules ]
; Compound#mols
DNA_chain_D 1
Protein_chain_L 1
Protein_chain_H 1
Now , I want to do a pulling simulation where , I want both chain L and
On 10/27/14 2:21 PM, fatemeh ramezani wrote:
Dear gmx-users
I built a graphene sheet (graphene.pdb ) by VMD. I convert it to gro file with
editconf command. Then I made top file with g_x2top command. But in top file
connection between atoms is not correct(highlighted lines below). How can I
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