Thank you Justin for giving your valuable time to solve
my stupid problems.
>>
> You can use either. I have never tried it, but there is no reason to
> believe there will be any substantive reason during data collection. The
> production MD period is significantly longer than the equilibration
On 5/28/12 4:09 PM, rama david wrote:
Thank you Justin..
Is these alternative process is right or totally wrong..???
Using the checkpoint in this instance is wrong. The only checkpoint you
have accessible to you at that point is from the end of the pulling
simulation a
Thank you Justin..
>> Is these alternative process is right or totally wrong..???
>>
>>
> Using the checkpoint in this instance is wrong. The only checkpoint you
> have accessible to you at that point is from the end of the pulling
> simulation and corresponds to the final state of the system.
On 5/28/12 3:49 PM, rama david wrote:
Thank you Justin for reply...
More or less. The special case with what you're doing in the tutorial is
that you have no initiating velocities in each window; you only have
coordinates. That's why it makes sense to do a bit of equilibration i
Thank you Justin for reply...
> More or less. The special case with what you're doing in the tutorial is
> that you have no initiating velocities in each window; you only have
> coordinates. That's why it makes sense to do a bit of equilibration in each
> window first, generating velocities and
On 5/28/12 3:12 PM, rama david wrote:
Thank you Thomas and Justin for your valuable suggestion.
Thomas and Justin, my Query is as follow..
In step six ..We are doing NPT equilibration followed by production run
The mdp files for both is same(Except the time of run and saving of output
> Thank you Thomas and Justin for your valuable suggestion.
> Thomas and Justin, my Query is as follow..
>
> In step six ..We are doing NPT equilibration followed by production run
> The mdp files for both is same(Except the time of run and saving of
> output)
> So why the two mdp are s
Thank you Thomas and Justin for your valuable suggestion.
Thomas and Justin, my Query is as follow..
In step six ..We are doing NPT equilibration followed by production run
The mdp files for both is same(Except the time of run and saving of
output)
So why the two mdp are same? Why
I think all the answers to your question are in the tutorial. Probably
read first the lysozyme tutorial and then the umbrella tutorial again.
But here is a more general answer:
Normally you have two types of simulations:
preperation (which is also equilibration)
production
and the need of rest
On Wed, May 23, 2012 at 7:30 PM, Du Jiangfeng (BIOCH) <
j...@maastrichtuniversity.nl> wrote:
> For your second problem: you have to create this file by writing the group
> numbers, which inform the script to decide which two groups
>
> Thank you... Du Jiangfeng
Yes problem get solve!!!
Thank yo
For your second problem: you have to create this file by writing the group
numbers, which inform the script to decide which two groups to be selected for
distance calculation.
If you made it, you first problem would probably be solved.
Good luck,
Jiangfeng.
Jiangfeng Du, PhD Student
C
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