Today I've tried to test gpu performance on the benchmark system (
explicit solvent with pme )
grompp-gpu -f md_sd.mdp -c conf -p topol.top -o md_test
mdrun-gpu -device
"OpenMM:platform=Cuda,DeviceID=1,Memtest=15,force-device=no" -v
-deffnm md_test
that produce the error
Program mdrun-gpu, VERSI
Dear Peter,
Would you please let me know how much time approximately the system of
protein/popc took to be npt-equilibrated sufficiently, in accordance with the
simulation you have reported in "Beyond modeling " paper.
In fact, I put the protein in popc and then ran NPT-equilibrium on i
Dear Peter,
Would you please let me know how much time approximately the system of
protein/popc took to be npt-equilibrated sufficiently, in accordance with the
simulation you have reported in "Beyond modeling " paper.
In fact, I put the protein in popc and then ran NPT-equilibrium on it f
On 1/6/13 8:39 PM, 라지브간디 wrote:
Dear users,
I want to know how to calculate
1. The rotation angle of helix moments ?
Probably g_principal does what you want.
2. number of water molecules interaction with ligand throughout the MD course ?
g_mindist can calculate contacts between any g
On 1/6/13 4:45 PM, Payman Pirzadeh wrote:
Hi,
I am using gromacs 4.5.4, and I am generating a topology file using G53a5
force field. My protein has a Cys residue which is supposed to be in
thiolate state (negatively charged side chain). During issuing the pdb2gmx
command I use the switch -inter
On 1/6/13 3:09 PM, Sanku M wrote:
Dear Gromacs users,
I am trying to perform a MD simulation in gromacs 4.5.4 using a protein and
ligand in gas phase.
I have previously run the simulation in water without any problem. Now, I want
to compare the result to see the effect of solvent.
But for
Dear users,
I want to know how to calculate
1. The rotation angle of helix moments ?
2. number of water molecules interaction with ligand throughout the MD course ?
Thanks in advance .
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Hi,
I am using gromacs 4.5.4, and I am generating a topology file using G53a5
force field. My protein has a Cys residue which is supposed to be in
thiolate state (negatively charged side chain). During issuing the pdb2gmx
command I use the switch -inter to be prompted about the charge state of the
You can construct such a subset after the fact by using trjconv with (say)
an index group created with g_select, but you will have to script that
process frame by frame yourself.
Mark
On Fri, Jan 4, 2013 at 9:35 PM, Justin Lemkul wrote:
>
>
> On 1/4/13 11:09 AM, Shima Arasteh wrote:
>
>> Dear u
Dear Gromacs users,
I am trying to perform a MD simulation in gromacs 4.5.4 using a protein and
ligand in gas phase.
I have previously run the simulation in water without any problem. Now, I want
to compare the result to see the effect of solvent.
But for running the same simulation after stri
On 1/6/13 1:53 PM, James Starlight wrote:
OK!
I've compilated gromacs-gpu from the source using that tutorial for
the Debian OS
http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html
The only thing that it lack is the installation mdrun_d-gpu but i'm
not sure that dou
OK!
I've compilated gromacs-gpu from the source using that tutorial for
the Debian OS
http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html
The only thing that it lack is the installation mdrun_d-gpu but i'm
not sure that double precission can be used with gpu.
Could so
On Sun, Jan 6, 2013 at 1:44 PM, James Starlight wrote:
> I mean absence of exponential factor in the C6 term :)
>
> So to change the vdw radius of the specified atom I should to varry
> both c6 and c12 shouldn't it ?
Hmm, to me these look like very basic force field questions. Did you
try to look
On 1/6/13 7:44 AM, James Starlight wrote:
I mean absence of exponential factor in the C6 term :)
Values can be represented as normal decimals or in scientific notation.
So to change the vdw radius of the specified atom I should to varry
both c6 and c12 shouldn't it ?
If you want to deri
On 1/6/13 7:41 AM, James Starlight wrote:
Have someone tried to use gromacs-4.5-gpu binaries ? Would that
packages work on debian or its better to build from sources ? :)
The binaries online are very outdated. Compiling from source is rather easy,
and the website below has all the steps li
On 1/6/13 7:29 AM, fatemeh ramezani wrote:
I didn't set epsilon and sigma between au and other atoms equal to zero, but I
have not enteredanyEpsilon and Sigmafor them , and once again I set them zero
and try it again.
If you didn't set them at all, grompp should have given a fatal error.
I mean absence of exponential factor in the C6 term :)
So to change the vdw radius of the specified atom I should to varry
both c6 and c12 shouldn't it ?
James
2013/1/5 Justin Lemkul :
>> so it may complicate such correction in that ff.
>>
>
> What's wrong with it?
>
>
> -Justin
>
> --
> =
Have someone tried to use gromacs-4.5-gpu binaries ? Would that
packages work on debian or its better to build from sources ? :)
James
2013/1/6 Justin Lemkul :
>
>
> On 1/6/13 4:48 AM, James Starlight wrote:
>>
>> Dear Gromacs Users!
>>
>>
>> I want to install gromacs 4.55 on my Debian OS with th
I didn't set epsilon and sigma between au and other atoms equal to zero, but I
have not enteredanyEpsilon and Sigmafor them , and once again I set them zero
and try it again.
But if closing of gold to protein, is because of charge, how do I delete its
effect ? How can I uncharged the system?
On 1/6/13 5:12 AM, fatemeh ramezani wrote:
Dear Justin
What you said is true for bonded parameters, but how about the parameters of
the nonbonded file?
Why Despite any non-bonded parameters (Sigma, Epsilon) are considered between
the gold atom and the other atoms , protein is stretched to t
On 1/6/13 4:48 AM, James Starlight wrote:
Dear Gromacs Users!
I want to install gromacs 4.55 on my Debian OS with the GPU support
(I'd like to make some calculations on the GeForce 670 gpu).
I have cuda-toolkit as well as openMM 4.01 installed from the binaries
as well as gromac's sources.
On 1/6/13 1:00 AM, Shima Arasteh wrote:
I ran NPT equilibration for 1ns. Would that be ok if I rerun it for 1 or more
ns ?
I have no idea what will be necessary for your system. That's up to you to
analyze and determine.
-Justin
--
Justin A. Le
Dear Justin
What you said is true for bonded parameters, but how about the parameters of
the nonbonded file?
Why Despite any non-bonded parameters (Sigma, Epsilon) are considered between
the gold atom and the other atoms , protein is stretched to the gold cluster ?
What is the reason for this
Dear Gromacs Users!
I want to install gromacs 4.55 on my Debian OS with the GPU support
(I'd like to make some calculations on the GeForce 670 gpu).
I have cuda-toolkit as well as openMM 4.01 installed from the binaries
as well as gromac's sources. Could you provide me with some tutorial
where
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