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
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
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
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 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
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?
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 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
>
> --
> =
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.
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 7:44 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 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
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 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
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
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
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
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
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
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 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
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
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
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