Justin,
You're right, the density of the box does increase during the simulation.
But I don't believe the water is particularly sparse, since I've never
encountered this issue in previous simulations, when I used these
parameters for genbox while inserting water. The system density also
appears to
Thank Tsjerk ! I mean that i want to determine the dimensions (x, y, z) of
the protein
On Fri, Feb 8, 2013 at 1:48 PM, Tsjerk Wassenaar wrote:
> Hi KT,
>
> What do you mean with size?
>
> - circumscribed radius: editconf
> - radius of gyration: g_gyrate
> - dimensions of fitting box: editconf
>
Hi KT,
What do you mean with size?
- circumscribed radius: editconf
- radius of gyration: g_gyrate
- dimensions of fitting box: editconf
- volume: g_sas
Cheers,
Tsjerk
On Fri, Feb 8, 2013 at 5:55 AM, Kieu Thu Nguyen wrote:
> Dear all,
>
> I want to calculate the size of the protein. Which too
I guess I will do mdrun -rerun 400 times then.
Thanks,
Yun
On Thu, Feb 7, 2013 at 9:06 PM, Bogdan Costescu wrote:
> On Thu, Feb 7, 2013 at 8:13 PM, Yun Shi wrote:
>> So instead of making an index file with 399 groups of each residue in
>> A and typing in rerun.mdp file 400 group names as
>> "en
On Thu, Feb 7, 2013 at 8:13 PM, Yun Shi wrote:
> So instead of making an index file with 399 groups of each residue in
> A and typing in rerun.mdp file 400 group names as
> "energygrps = A1 A2 A3 A4 ... A399 B", and issuing g_energy command 399 times,
There can be maximum 256 groups defined at on
Dear all,
I want to calculate the size of the protein. Which tool should i use for
this purpose ?
Thanks and regards,
KT
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Hi,
If you have two GTX 590-s four devices should show up in nvidia-smi and
mdrun should also show four devices detected. As nvidia-smi shows only two
GPUs means that one of your cards is not functioning properly.
You can try to check what GPU devices does you operating system "see"
independently
On 2/7/13 2:56 PM, S. Alireza Bagherzadeh wrote:
Dear Justin,
Today's Topics:
1. Re: Translating my system using editconf causes my runto
crash! (Justin Lemkul)
--
Message: 1
Date: Wed, 06 Feb 2013 20:54:01
On 2/7/13 2:29 PM, Davide Mercadante wrote:
Thank you Justin,
I guess this means that this kind of simulations is not possible without a
modification of the forcefield (which would ultimately mean using a
different forcefield I believe)?
If you're looking to unfold secondary structure eleme
Thank you Justin,
I guess this means that this kind of simulations is not possible without a
modification of the forcefield (which would ultimately mean using a
different forcefield I believe)?
Thanks.
Cheers,
Davide
On 7/02/13 8:09 PM, "Justin Lemkul" wrote:
>
>
>On 2/7/13 1:44 PM, Davide
On 2/7/13 2:13 PM, Yun Shi wrote:
Hi all,
I want to rerun a trajectory to calculate interaction energies between
each residue of protein A and protein B. In other words, I want to
calculate interaction energies for pairs A1 - B, A2-B, A3-B, A4-B...,
A399-B.
So instead of making an index file
On 2/7/13 1:44 PM, Davide Mercadante wrote:
Dear Justin,
Thank you for your reply. I decreased the time step from 0.02 to 0.005 and
run the simulation again. The simulation still crashes giving LINCS
warning on the same atoms but does it later.
Do you advice to keep reducing the time step in o
Dear Justin,
Thank you for your reply. I decreased the time step from 0.02 to 0.005 and
run the simulation again. The simulation still crashes giving LINCS
warning on the same atoms but does it later.
Do you advice to keep reducing the time step in order to reach a simulated
time where the pull o
On 2/7/13 12:40 PM, Yun Shi wrote:
A general question:
In COM pulling (pull two molecules away), does the weakest
inter-molecular interaction always break first? Or is it the
interaction aligned on the pulling direction break first?
Probably both. Whatever you do with SMD is path-dependent
On 2/7/13 12:39 PM, jeela keel wrote:
Hi All,
Thank you for the help. But I am not sure how to use cmake?? Do I need to
make a new directory something like the following, or just in the gromacs
directory?
mkdir cmake
cd cmake
cmake -DCMAKE_PREFIX_PATH=/home/jeela/local/gromacs-4.6
--progra
A general question:
In COM pulling (pull two molecules away), does the weakest
inter-molecular interaction always break first? Or is it the
interaction aligned on the pulling direction break first?
In other words, does every part of the molecule "feel" the pulling
force? Or the part close to the
Hi All,
Thank you for the help. But I am not sure how to use cmake?? Do I need to
make a new directory something like the following, or just in the gromacs
directory?
mkdir cmake
cd cmake
cmake -DCMAKE_PREFIX_PATH=/home/jeela/local/gromacs-4.6
--program-suffix=-4.6 --with-fft=fftw3
Thank you
Hi Anthony,
just one remark here: Make sure you have always a couple of histograms
overlapping each other (maybe 5-10). If every histogram overlaps only
with two neighbors, you will severely underestimate the error.
Hence, to estimate the error, you need rather many histograms from many
shor
Hello,
Is it correct for you that in your topolgy file, some atoms have wrong mass
(i.e. C7 and C9 have a mass of 15.035 instead of 14.027) in your DECAN
molecule ? Are they at the end ?
Stephane
--
Message: 3
Date: Thu, 7 Feb 2013 19:13:11 +0330
From: Ali Al
On 02/07/2013 01:34 PM, Szilárd Páll wrote:
Please make sure that nvididia-smi or the deviceQuery SDK tool show all
four GPUs. If that is the case and mdrun still shows only two, please file
a bug report with you OS info and a log file attached.
Cheers,
--
Szilárd
no, it showed two. I don't kn
On 2/7/13 10:43 AM, Ali Alizadeh wrote:
Dear Justin
Thank you for your reply,
I want to use Nose-Hoover thermostat and MTTK barostat and shake
algorithm and md-vv integrator,
but I got this error:
---
Fatal error:
SHAKE is not supported with domain decomposit
Ah, now perhaps I see that I misread the question - it could have been
phrased more clearly. If Erik understood it correctly, then the
answer to the question is: It depends on the integrator. The
simulation is not constrained to a particular temperature or pressure
- rather, the dynamics are modi
On 2/7/13 9:46 AM, Ali Alizadeh wrote:
Dear All user
There are 350 decane molecules in my simulation box,
I like doing a simulation(npt ensemble) by a united atom force field,
Can I use the opls (nonbonded: L-J 6-12 and coloumb) that is in
gromacs?
Beside, How can I neglect coloumb interact
Thank you,
My intention is mainly to compare the MSDs of the
trajectory and not the diffusion as such. The paper I
mentioned have used a tetramer for the similar analysis.
Hence I wanted to know whether the values I obtained
is sensible.
Thank you
Kavya
On Thu, Feb 7, 2013 at 7:25 PM, Justin Lem
On 2/7/13 7:08 AM, Kavyashree M wrote:
Dear Sir,
Yes it is the same protein. Initially I had not superposed the
structures in the trajectory. But this time I calculated the msd
on a superposed trajectory (of the same simulation). the simulation
is carried out on a dimer for 50ns using OPLS-AA
On Thu, Feb 7, 2013 at 10:16 AM, Albert wrote:
> Hello:
>
> I got a workstation with two GTX590 which have two core for each GPU. I
> can submit gromacs GPU jobs with command:
>
> mpirun -np 4 mdrun .
>
> with such running, I can get 26ns/day for Gromacs-4.6 beta version.
>
> However, I fou
Thank you,
I have noticed this in the output of the g_saltbr. Later
I separated the files according to what ever I require.
My worry was only that of the dimeric interface which
could not be seen because it is separated.
I will try by giving a separate tpr file without water.
Thank you
Kavya
O
Dear Sir,
Yes it is the same protein. Initially I had not superposed the
structures in the trajectory. But this time I calculated the msd
on a superposed trajectory (of the same simulation). the simulation
is carried out on a dimer for 50ns using OPLS-AA and TIP4P water
model. Using Gromacs4.5.3.
On 2/7/13 5:20 AM, Davide Mercadante wrote:
Dear All,
I am trying to run a pulling simulation on a small protein (18 aa) using
the GC forcefield MARTINI (v2.2). I have energy minimized and
equilibrated (NPT) my system and everything seems fine. My system
consists of the protein + water + ions
On 2/7/13 5:16 AM, Steven Neumann wrote:
Dear Gmx users,
I know this subject has been discussed but I still did not find the answer.
I have topology of my molecule:
ligand.rtp
[ GUY ] ; CGenFF output = RESI aR_citri 0.000 ! param penalty= 46.200
; charge penalty= 28.481
[ atoms ]
C1
On 2/7/13 5:15 AM, James Starlight wrote:
Justin,
Thanks again for suggestion. I've found that g_mindist is exactly what
I need. I'm not quite sure how I could use that tools to find all
possible interactions between my ligand and several polar residues
defined in the ndx file ( I have no prob
On 2/7/13 6:42 AM, Kavyashree M wrote:
Dear users,
After simulation dimers appear separated, I was
able to do saltbridge calculation on this. This will
be different than doing it on a dimer which are together.
Am I correct?
Most Gromacs tools handle PBC well for simple metrics like measurem
On 2/7/13 6:49 AM, Kavyashree M wrote:
Dear Sir,
Thank you for the reply,
It does not cross the boundary. I made the trajectory
so that the dimers are together.
I again calculated on a superposed trajectory, Then I
got MSDs in the range of 0.01 to 0.15nm^2. But this
is still higher than the
On 2/7/13 4:50 AM, Shima Arasteh wrote:
Thanks for your reply.
How would I know that when I get close to the equilibration state? By
Pressure, Temperature,or RMSD plots?
There are no absolutes, and it also depends on what one means by "converged" or
"equilibrated." If we're talking abo
Dear Sir,
Thank you for the reply,
It does not cross the boundary. I made the trajectory
so that the dimers are together.
I again calculated on a superposed trajectory, Then I
got MSDs in the range of 0.01 to 0.15nm^2. But this
is still higher than the value mentioned in the paper or
is this acc
Dear users,
After simulation dimers appear separated, I was
able to do saltbridge calculation on this. This will
be different than doing it on a dimer which are together.
Am I correct?
Please reply..
Thank you
Kavya
On Thu, Feb 7, 2013 at 3:39 PM, Kavyashree M wrote:
> Dear users,
>
> While c
On 2/7/13 4:19 AM, Bharath K. Srikanth wrote:
Hi Justin:
Thanks for your reply. Yes, I did everything you mentioned. Let me explain
my steps in a bit more detail.
1) I had a lipid bilayer and a peptide from a previous simulation (in a
box 15 nm x 7.5 nm x 7.5 nm- 15 nm being perpendicular to
On 2/6/13 11:49 PM, Kavyashree M wrote:
Dear users,
Since I am getting the mean square displacements in terms of
several nm^2. I doubt it is wrong. Could anyone please explain
me the solution for this. I checked the structure it is not denatured,
In addition I used -rmcomm in order to remove t
Hi,
You don't need SLI for multi-GPU simulations in Gromacs.
But you do need a real MPI library and configure Gromacs with -DGMX_MPI=on
Then you need to start Gromacs with (depending on you MPI library):
mpirun -np #GPUs mdrun
If anything, the performance of Gromacs should have gotten better fro
On 02/07/2013 11:28 AM, James Starlight wrote:
Also could you tell me what your system has performance (in gflops)
and what system you have simulated on it (average atom number,
presence of explicit membrane etc)?
it is something around 55,000 atoms with explicit membrane. I am using
Slipids F
Albert,
thanks for information!
So now it's only intresting to my how I should install multi-GPU's on
my system to obtain best compatibility with gromacs.
Also could you tell me what your system has performance (in gflops)
and what system you have simulated on it (average atom number,
presence o
On 02/07/2013 11:03 AM, James Starlight wrote:
Hi Albert!
As I understood your correctly you have run simulations with your 2
GPU cards on Gromacs-beta but could not do it with final version
havent it?
not really. both versions could run with GPU. The 4.6 beta recognize my
number of GPU as 4,
Dear All,
I am trying to run a pulling simulation on a small protein (18 aa) using
the GC forcefield MARTINI (v2.2). I have energy minimized and
equilibrated (NPT) my system and everything seems fine. My system
consists of the protein + water + ions NA+ and CL-.
After the equilibration I start a
Justin,
Thanks again for suggestion. I've found that g_mindist is exactly what
I need. I'm not quite sure how I could use that tools to find all
possible interactions between my ligand and several polar residues
defined in the ndx file ( I have no problem only when I examined
manually each possibl
Hi Albert!
As I understood your correctly you have run simulations with your 2
GPU cards on Gromacs-beta but could not do it with final version
havent it?
Could you tell me how you installed both GPU in your work-station?
Have you used SLI ? ( I've heard that gromacs is not suported the
simulati
Thanks for your reply.
How would I know that when I get close to the equilibration state? By
Pressure, Temperature,or RMSD plots?
Thanks in advance for your suggestions.
Sincerely,
Shima
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
Hi Justin:
Thanks for your reply. Yes, I did everything you mentioned. Let me explain
my steps in a bit more detail.
1) I had a lipid bilayer and a peptide from a previous simulation (in a
box 15 nm x 7.5 nm x 7.5 nm- 15 nm being perpendicular to the plane of the
bilayer). I removed the water and
Hello:
I got a workstation with two GTX590 which have two core for each GPU.
I can submit gromacs GPU jobs with command:
mpirun -np 4 mdrun .
with such running, I can get 26ns/day for Gromacs-4.6 beta version.
However, I found that for Gromacs-4.6 final version (which is the latest
on
I've never seen good parameters for nucleic acids. There might be
such, but none that ship with gromacs as far as I know.
Erik
On Feb 7, 2013, at 4:25 AM, 김현식 wrote:
Dear experts,
Hello!
Is it possible to run RNA md with GBSA?
Thank you.
bestKim. --
Dear Silard,
cmake -DGMX_CPU_ACCELERATION=AVX_256 -DGMX_DEFAULT_SUFFIX=OFF
-DGMX_BINARY_SUFFIX="_avx" -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_DOUBLE=ON
-DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl
-DMKL_INCLUDE_DIR=$MKLROOT/include
-DMKL_LIBRARIES="$MKLROOT/lib/intel64/libmkl_core.
Hi,
Perhaps a side point: Temperature and pressure can not be seen as
constraints to the system at any given instant in the sense that e.g.
the instantaneous kinetic energy perfectly match the temperature at
every time step just because you have a thermostat. Time and ensemble
averages wi
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