g_sham calculates free energy landscapes by computing the joint
probability distribution from the two dimensional plane constructed
using two quantities (in your case it will be rmsd and radius of
gyration). Conformations sampled during the simulation were projected
on this two dimensional plane, a
Dear users,
Can someone kindly explain how g_sham calculates
the free energy landscape of given two quantities say,
rmsd and radius of gyration.
Any references are welcome.
Thank you
with Regards
Kavya
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On 3/30/13 11:47 AM, Elisabeth wrote:
Hi Justin,
The corect value is 3.5e-5 but I thoiugh x/y means the ratio od these two.
No, it is not a ratio. The use of "x/y" simply means both x and y.
If thats nto the case I guess compressibility = 3.5e-5 0 is the
correct value. What do you th
Hi Justin,
The corect value is 3.5e-5 but I thoiugh x/y means the ratio od these two.
If thats nto the case I guess compressibility = 3.5e-5 0 is the
correct value. What do you think?
On 30 March 2013 11:41, Justin Lemkul wrote:
>
>
> On 3/30/13 11:39 AM, Elisabeth wrote:
>
>> Hi all,
>>
>
On 3/30/13 11:39 AM, Elisabeth wrote:
Hi all,
I wanted to use Pcoupltype = semiisotropicbut I am not clear
about the compressibility settings if I want to keep Z directions fixed in
my system and letting X and Y change. Which case 1 or 2 is correct for semi
isotropic option?
1)
Hi all,
I wanted to use Pcoupltype = semiisotropicbut I am not clear
about the compressibility settings if I want to keep Z directions fixed in
my system and letting X and Y change. Which case 1 or 2 is correct for semi
isotropic option?
1) compressibility = 3.5e-5 3.5e-5 0
2
On 3/30/13 10:21 AM, aixintiankong wrote:
Dear,
I have install intel icc and ifor on my system centos, and i want to install
gromacs4.6.1 using the intel icc and ifor,please help me what flag i should use
to indicate the icc and ifor when i install the gromacs.
-DCMAKE_C_COMPILER=icc -DCMAK
Dear,
I have install intel icc and ifor on my system centos, and i want to install
gromacs4.6.1 using the intel icc and ifor,please help me what flag i should use
to indicate the icc and ifor when i install the gromacs.
thank you very much!
At 2013-02-21 13:00:55,aixintiankong wrote:
Dear
Hi,
You can certainly use your hardware setup. I assume you've been looking at
the log/console output based on which it might seem that mdrun is only
using the GPUs in the first (=master) node. However, that is not the case,
it's just that the current hardware and launch configuration reporting is
I'm running Gromacs 4.6.1 on 2 nodes with 3 GPUs(2 on host1,1 on host2,
all nvidia K20c), and I'm using openMPI 1.6.4 to let Gromacs run parallel
on 2 nodes. However, I found that Gromacs can only find the GPUs on the
local node which it's launched, it can't automatically use the GPUs on the
other
Dear Gromacs Specialists,
I want to find information about RDF of some components in my system but when I
do the g_rdf command, I find true answers about RDF diagrams but my system type
below note in several times:
"There were 2 inconsistent shifts. Check your topology"
May I know that this mess
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