Thank you very much
I understood completely
Best
On Sun, May 8, 2011 at 7:30 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> Thank you for your complete explanation.
>> Please let me discribe where is NPT.cpt comes from:
>>
>> Before doing Pulling step,I d
mohsen ramezanpour wrote:
Dear Dr.Justin
Thank you for your complete explanation.
Please let me discribe where is NPT.cpt comes from:
Before doing Pulling step,I did an NPT step (as your tutorial) to
generate NPT ensemble.
the outputs of this step were NPT.cpt, NPT.gro and NPT.enr and ..
Dear Dr.Justin
Thank you for your complete explanation.
Please let me discribe where is NPT.cpt comes from:
Before doing Pulling step,I did an NPT step (as your tutorial) to generate
NPT ensemble.
the outputs of this step were NPT.cpt, NPT.gro and NPT.enr and ...
Then I used NPT.gro for Pulli
mohsen ramezanpour wrote:
Dear Dr.Justin
I didn't any equilibration for any windows! Because:
As I know the thermodynamics of the system had wroten in NPT.cpt file
(for example the velocities and etc).
Then where does NPT.cpt come from? Presumably, if you have this file, you did
some equi
Dear Dr.Justin
I didn't any equilibration for any windows! Because:
As I know the thermodynamics of the system had wroten in NPT.cpt file (for
example the velocities and etc).
Then when I use that in grompp for each windows ,I expect the same
characteristics of system as before(At least the same
mohsen ramezanpour wrote:
Dear Dr.Justin
Regarding doing umbrella sampling:
I used gen_vel =no
and I prefer to use from thermodynamics of system in NPT.cpt
Although the T and P were as I did set in NPT.mdp file (T=310 ,P=1 bar)
But their values in my umbrela.log files are not as before (for
Dear Dr.Justin
Regarding doing umbrella sampling:
I used gen_vel =no
and I prefer to use from thermodynamics of system in NPT.cpt
Although the T and P were as I did set in NPT.mdp file (T=310 ,P=1 bar)
But their values in my umbrela.log files are not as before (for example
P=-8.434578e+1)
Wher
Thank you very much Dr.Justin for your important notes
On Wed, Apr 6, 2011 at 8:09 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>> I had asked this question before but unfortunately I didn't answered
>> good!
>>
>> Instead of Pulling and separating some struc
mohsen ramezanpour wrote:
Dear Dr.Justin
I had asked this question before but unfortunately I didn't answered good!
Instead of Pulling and separating some structures in definite distances,
I located my drug in definite distances along z axis (as my initial
structures for doing umbrella sam
Dear Dr.Justin
I had asked this question before but unfortunately I didn't answered good!
Instead of Pulling and separating some structures in definite distances,
I located my drug in definite distances along z axis (as my initial
structures for doing umbrella sampling).
Am I right?
The main pro
Mohsen:
To be honest, this just sounds like debating. I have offered you my
perspective already.
Chris.
-- original message --
Dear chris
Thanks for your reply
1-I am not sure,Since we need the know the variations of free energy along a
specific degree of freedom of system(for example z ax
Dear chris
Thanks for your reply
1-I am not sure,Since we need the know the variations of free energy along a
specific degree of freedom of system(for example z axis),so the springs
must be 1 dimensional to allow drug to oscilate only in one dimension(z
axis).
Let me say my question in other word
1. Depends on how you set them in your .mdp file. It could be either.
2. There is no general method. Use trial and error. Also, your
question is flawed, K defines X. Unless by "length of one windows" you
meant the distance between neighbouring centers of restraint
(umbrellas).
3. you need
Dear All
afew question in umberella sampling tutorial:
1-We do umberella sampling for each of 25 simulation windows,while using a
spring(harmonic potential),Are these springs 1 or 3 dimensional?
2-Suppose the length of one windows is X nm,what is the approperiate K
(spring constant) for this wind
mohsen ramezanpour wrote:
Dear All and Specially Dear justin
After reading umberella sampling tutorial I have afew question.
Please let me know their answers.
1-How did you realized(What was your criteria) the range of 0.5 -5 nm is
enough? it might be different if you chose 0.2-5 nm.Am I ri
Dear All and Specially Dear justin
After reading umberella sampling tutorial I have afew question.
Please let me know their answers.
1-How did you realized(What was your criteria) the range of 0.5 -5 nm is
enough? it might be different if you chose 0.2-5 nm.Am I right?
2-The histogram showes a
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
-- original message --
I can't understand correctly what we do when we are using umberella sampling
for obtaining PMF.
I explain that ,please modify or complete it.
(I think we define some sampling windo
Dear All
I can't understand correctly what we do when we are using umberella sampling
for obtaining PMF.
I explain that ,please modify or complete it.
(I think we define some sampling windows,each related to an reference
distance.
for each distance ,relative to it's distance,we define a spring c
mohsen ramezanpour wrote:
Dear All And Specially Dear Justin
I read the toturial of Umbrella Sampling.It was very useful
But there are afew question,of course about my work .
1-Is it necessary pulling one molecule along the line connecting their
COMs?
The pull code is based on COM distanc
Dear All And Specially Dear Justin
I read the toturial of Umbrella Sampling.It was very useful
But there are afew question,of course about my work .
1-Is it necessary pulling one molecule along the line connecting their COMs?
2-I have a protein-drug complex,it has oriented in a ordinary directi
20 matches
Mail list logo
