have now negative distances in pullx.xvg. I don't know if the fact that
we now have negative numbers makes any problem for WHAM (from the *.tpr
we would expect that we have only positive numbers).
Wish you luck.
greetings
thomas
Date: Tue, 10 Jan 2012 10:47:43 +0000
From: Gavin Mela
ian, you
> couldn't say anything.
>
>
>
>> Date: Tue, 10 Jan 2012 10:47:43 +0000
>> From: Gavin Melaugh
>> Subject: Re: [gmx-users] RDF(PMF) and Umbrella sampling
>> To: Discussion list for GROMACS users
>> Message-ID:<4f0c174f.2050...@qub.ac.uk>
distances. For this case it would be easy to correct the
histogram. But if the histogram isn't a perfect gaussian, you couldn't
say anything.
Date: Tue, 10 Jan 2012 10:47:43 +
From: Gavin Melaugh
Subject: Re: [gmx-users] RDF(PMF) and Umbrella sampling
To: Discussion list for GRO
Hi Justin
Again, many thanks for the reply.
So when the COM distance changes sign, what effect does that have on the
distribution of the COM distance about the mean value for that window
i.e. If say my ref dist in 0 nm and the umbrella sampling allows the
distance to sample distances say at 0.02 n
Gavin Melaugh wrote:
Hi Justin
Thanks very much. One last question. What do you mean when you say "COM
reference distance is changing signs"? I thought the COM distance was
the absolute distance between the two groups and therefore cannot be
negative?
The pull code deals in vectors. Signs
Hi Justin
Thanks very much. One last question. What do you mean when you say "COM
reference distance is changing signs"? I thought the COM distance was
the absolute distance between the two groups and therefore cannot be
negative?
Cheers
Gavin
Dariush Mohammadyani wrote:
> Hi Gavin,
>
> A ques
Gavin Melaugh wrote:
Hi Justin
Just a quick clarification regarding my previous point. With geometry =
distance, and pull_dim =Y Y Y . Is the pull_group sampling all
dimensions equally (or without prejudice) about pull_init ? And iN your
I don't necessarily know if you can say "equally," bu
Dariush Mohammadyani wrote:
Hi Gavin,
A question arose for me: why did you consider the (rate = 0)?
During umbrella sampling one restrains the configuration; you don't steer it
along the vector between the COM's of the two species.
-Justin
--
Ju
Hi Gavin,
A question arose for me: why did you consider the (rate = 0)?
Dariush
On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaugh wrote:
> Hi Justin
>
> Just a quick clarification regarding my previous point. With geometry =
> distance, and pull_dim =Y Y Y . Is the pull_group sampling all
> dime
Hi Justin
Just a quick clarification regarding my previous point. With geometry =
distance, and pull_dim =Y Y Y . Is the pull_group sampling all
dimensions equally (or without prejudice) about pull_init ? And iN your
first reply what did you mean about by "straight pull" ?
Cheers
Gavin
Justin
O.K cheers
Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> Thanks for the reply. I wanted my "pulling" to be free in all
>> directions, that is in the liquid state with no defined reaction
>> coordinate i.e not along a specific axis. This is why I used geometry =
>> distance.
Gavin Melaugh wrote:
Hi Justin
Thanks for the reply. I wanted my "pulling" to be free in all
directions, that is in the liquid state with no defined reaction
coordinate i.e not along a specific axis. This is why I used geometry =
distance. Would you agree with this approach?
I suppose there
Hi Justin
Thanks for the reply. I wanted my "pulling" to be free in all
directions, that is in the liquid state with no defined reaction
coordinate i.e not along a specific axis. This is why I used geometry =
distance. Would you agree with this approach?
By free I mean. The absolute distance betwe
Gavin Melaugh wrote:
Dear all
I have a query regarding umbrella sampling simulations that I have
carried out to study a dynamical process of a guest inserting into a
host. I always get get a wall tending off to infinity at or just before
the zero distance between the
two species.
The process I
Dear all
I have a query regarding umbrella sampling simulations that I have
carried out to study a dynamical process of a guest inserting into a
host. I always get get a wall tending off to infinity at or just before
the zero distance between the
two species.
The process I describe, for one system
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