Dear Emanuel,
Here are a few comments that may help your way through the literature
already pointed out by others.
Most of your questions concern temporal/kinetic aspects (interchange
times, etc) and the answer to them is quite simple: constant-pH MD
methods are intended to produce a collec
>
> Message: 1
> Date: Wed, 07 Sep 2011 12:01:00 +0200
> From: "Emanuel Peter"
> Subject: Antw: Re: Antw: Re: Re: [gmx-users] constant PH simulations
> To:
> Message-ID: <4e675cfc02f100014...@gwsmtp1.uni-regensburg.de>
> Content-Type: text/plain; ch
SMA.
>>> João Henriques 07.09.11 13.09 Uhr >>>
Why don't you read the papers associated with the link everyone keeps
sending you!!!
Stop it with the autistic behavior.
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
Here is the main paper regarding the CpH-MD method I'm curre
Why don't you read the papers associated with the link everyone keeps
sending you!!!
Stop it with the autistic behavior.
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
Here is the main paper regarding the CpH-MD method I'm currently using:
http://jcp.aip.org/resource/1/jcpsa
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
On 7 September 2011 11:01, Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> wrote:
> At first I would like to say that I deeply apologize for
> the cave-like things I have said. I again say, that this
> was not the field I
At first I would like to say that I deeply apologize for
the cave-like things I have said. I again say, that this
was not the field I am deeply involved.
>From Gerrit I got a banana.
For this guy, I am a cave-man.
Thanks, for being such ready for open discussion.
I did not tell that I do not wa
There is no problem in being wrong. The problem is that he wants to be
wrong. At least 4 different researchers gave constructive input and
this subject keeps hitting the same key. I've always been told that
worse than not knowing, is not wanting to know.
Still, I apologize for my outburst.
Best r
, Gerrit.
>>> Gerrit Groenhof 06.09.11 19.06 Uhr >>>
>
> 2. Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter)
>
> Message: 2
> Date: Tue, 06 Sep 2011 15:49:28 +0200
> From: "Emanuel Peter"
> Subject: Antw: Re: Re: [gmx-u
On 7/09/2011 3:53 AM, João Henriques wrote:
I guess someone has been living in a cave for the past decade or so...
Please keep contributions to the mailing list constructive :-)
Everyone's been wrong before!
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mai
"No forcefield on whole earth is able to reproduce the pH realistically
by H+.
You just can apply pH of your system through the protonation states
of each part in your system."
I guess someone has been living in a cave for the past decade or so...
Cheers,
--
João Henriques
--
gmx-users mailing l
>
> 2. Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter)
>
> Message: 2
> Date: Tue, 06 Sep 2011 15:49:28 +0200
> From: "Emanuel Peter"
> Subject: Antw: Re: Re: [gmx-users] constant PH simulations
> To:
> Message-ID: <4e66410802
Emanuel Peter wrote:
The standard procedure of H+ interchange and transition states can be done
through QM/MM.
Please give one reference according to the algorithms you have mentioned.
There are several cited at:
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
-Justin
The standard procedure of H+ interchange and transition states can be done
through QM/MM.
Please give one reference according to the algorithms you have mentioned.
Cheers.
>>> João M. Damas 06.09.11 15.19 Uhr >>>
As Justin said, constant protonation != constant pH.
Constant-pH MD does not simul
As Justin said, constant protonation != constant pH.
Constant-pH MD does not simulate H+, but allows changes in protonation
states during the MD simulation. There are different algorithms
to accomplish that.
Cheers,
João
On Tue, Sep 6, 2011 at 2:04 PM, Emanuel Peter <
emanuel.pe...@chemie.uni-re
Emanuel Peter wrote:
Could you just tell me smth. !
No forcefield on whole earth is able to reproduce the pH realistically
by H+.
You just can apply pH of your system through the protonation states
of each part in your system.
Constant protonation state and constant pH are different. Gromac
Could you just tell me smth. !
No forcefield on whole earth is able to reproduce the pH realistically
by H+.
You just can apply pH of your system through the protonation states
of each part in your system.
monkey.
>>> João M. Damas 06.09.11 14.22 Uhr >>>
That is not considered constant-pH MD.
That is not considered constant-pH MD.
Follow Justin's suggestion.
Cheers,
João
On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> wrote:
>
> Look for the pKa-constants of each part of your system (e.g. each
> amino-acid).
> Then you can check each protonat
fancy2012 wrote:
Dear gmx users,
Are there some tutorials on constant PH simulations using gromacs? How
should I state my work? Right now I have no idea on it.
Interestingly enough, there is a page devoted to this topic on the Gromacs wiki:
http://www.gromacs.org/Documentation/How-tos/
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