Re: [gmx-users] Free energy landscape by g_sham

[bipin singh]

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, and the number of points occupied by
each cell was counted. The grid cell containing the maximum number of
points is then assigned as the reference cell, with a free energy
value of zero. Free energies for all the other cells were assigned
with respect to this reference cell using the following equation:

ΔG = -kbT ln P(x,y)/Pmin

P(x,y) is the estimate of probability density function obtained from a
histogram of MD data and  Pmin is the maximum of the probability
density function. Kb is the Boltzmann constant, and T is the
temperature corresponding to each simulation.


On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M  wrote:
> 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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Thanks and Regards,
Bipin Singh
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[gmx-users] Free energy landscape by g_sham

[Kavyashree M]

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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Re: [gmx-users] semi isotropic settings

[Justin Lemkul]

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 think?



Sounds more reasonable.

-Justin


On 30 March 2013 11:41, Justin Lemkul  wrote:




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) compressibility =  3.5e-5 3.5e-5 0

2 ) or compressibility =  1 0?
Manual says 2 values are needed for x/y and z directions respectively.



Case #2, though I doubt a value of 1 is a correct compressibility.  But as
the manual says, you need two values - one for x/y (i.e. those two
dimensions are equally compressible) and one for z.

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin

==**==
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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] semi isotropic settings

[Elisabeth]

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,
>>
>> 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 ) or compressibility =  1 0?
>> Manual says 2 values are needed for x/y and z directions respectively.
>>
>>
> Case #2, though I doubt a value of 1 is a correct compressibility.  But as
> the manual says, you need two values - one for x/y (i.e. those two
> dimensions are equally compressible) and one for z.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] semi isotropic settings

[Justin Lemkul]

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) compressibility =  3.5e-5 3.5e-5 0

2 ) or compressibility =  1 0?
Manual says 2 values are needed for x/y and z directions respectively.



Case #2, though I doubt a value of 1 is a correct compressibility.  But as the 
manual says, you need two values - one for x/y (i.e. those two dimensions are 
equally compressible) and one for z.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] semi isotropic settings

[Elisabeth]

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 ) or compressibility =  1 0?
Manual says 2 values are needed for x/y and z directions respectively.

Thanks
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Re: [gmx-users] how to install the gromacs 4.6.1 using the intel icc and ifor

[Justin Lemkul]

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 -DCMAKE_CXX_COMPILER=icpc

Alternatively, I think you can set CC and CXX environment variables.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] how to install the gromacs 4.6.1 using the intel icc and ifor

[aixintiankong]

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,
there are three waters in active site of receptor,mediating the binding of 
ligand with target protein. i want to study the three waters how to affect the 
binding of ligand with target protein and the contribution to the stability of 
the system.
   In order to avoid the three waters exchange with the solvent waters, how to 
constrain solvent waters adding in active site when i solvate protein and 
diffusing in active site during diffuse dynamic simulation. can i set some 
parameters in mdp file to slove the problem? 

 

 





 


 Forwarding messages 
From: aixintiankong 
Date: 2013-02-16 23:54:51
To: gmx-users@gromacs.org
Subject: some waters in active site of receptor

Dear,
 there are three waters in active site of receptor, mediating the binding 
of ligand with target protein. i want to study the three waters how to affect 
the binding of ligand with target protein and the contribution to the stability 
of the system.
 In order to study the role of the waters, i want to compare some diffrent 
system models. The first model have all a waters in active site ,the second 
model have two waters and the third have one water , the fourth have none water 
in acitve site. however, i don't know how to construct simulation models  of 
those. when i use the genbox program to add solvent to my system,  i find there 
are many other waters being added to the active site and i think the waters 
which are added by genbox program  maybe replace the initial three waters and 
then i can't study the waters in active site.
 please hlpe me and then tell me how to do it
Thank you very much!








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Re: [gmx-users] About the configuration of Gromacs on multiple nodes with GPU

[Szilárd Páll]

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
unfortunately not very flexible and it assumes homogeneous hardware and run
configuration. Whatever gets printed to the console and log shows *only*
information related to the master node. Hence, if you have inhomogeneous
hardware with different CPUs or GPUs, mdrun will try to use all resources -
as long as your launch configuration allows it.

If you want to run across inhomogeneous node configurations, you can pass
node-specific launch/run parameters to mdrun using separate environment
variables per node - the GMX_GPU_ID environment variable to set the GPUs
per node to be used and OMP_NUM_THREADS to set manually set the number of
threads per rank. What you'd need to do is to write a wrapper around mdrun
which will set GMX_GPU_ID=01 on the first node and GMX_GPU_ID=0 (or "00",
for the details see http://goo.gl/a3ZMi).

Cheers,

--
Szilárd


On Sat, Mar 30, 2013 at 10:19 AM, 崔学文  wrote:

>  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 node.
>  I've been wondering whether current version of Gromacs support such kind
> of configuration(multiple GPUs on multiple nodes). Could you please give me
> some advice on how to fix this problem?
>
>   With many thanks.
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[gmx-users] About the configuration of Gromacs on multiple nodes with GPU

[崔学文]

 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 node.
 I've been wondering whether current version of Gromacs support such kind
of configuration(multiple GPUs on multiple nodes). Could you please give me
some advice on how to fix this problem?

  With many thanks.
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[gmx-users] g_rdf

[mohammad agha]

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 message is important or not, Please?
If this message is important, Please help me to solve this problem.


Best Regards
Sara
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