On Tue, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang wrote:
> Dear gmx-users,
>
> Could anyone help me with the calculation of 3D pressure profile in a
> function of y?
> I used the provided gromacs-4.0.2_localpressure for my calculatioin. It
> calculate
> the 3D pressure profile as a function of z (
On Wed, Sep 7, 2011 at 12:11 AM, Amit Choubey wrote:
>
>
> On Tue, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang wrote:
>
>> Dear gmx-users,
>>
>> Could anyone help me with the calculation of 3D pressure profile in a
>> function of y?
>> I used the provided gromacs-4.0.2_localpressure for my calculat
On Wed, Sep 7, 2011 at 12:30 AM, Shou-Chuang Yang wrote:
>
>
> On Wed, Sep 7, 2011 at 12:11 AM, Amit Choubey wrote:
>
>>
>>
>> On Tue, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang wrote:
>>
>>> Dear gmx-users,
>>>
>>> Could anyone help me with the calculation of 3D pressure profile in a
>>> function
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
Hi Florian,
I have followed your suggestion below and used a pdb file instead of a xtc
file and it works!!! Thank you very much for the info.
A bientot
Stephane
--
Message: 3
Date: Tue, 06 Sep 2011 12:26:34 +0200
From: Dommert Florian
Subject: Re: [gmx-users] F
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
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
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
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
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor.
karthick wrote:
sir
iam karthick using gromacs for academic purpose.i had run protein-ligand
complex based on your lyzozyme tutorial.further i want to about DGbind
value..i heard g_lie comm
>
> 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; charset="iso-8859-1"
>
> At first I would li
Dear friends,
I am using the GROMACS-4.5.3 for molecular dynamics as described by* Justin
Lemkul in Tutorial 2: KALP15 in DPPC. *I want to calculate the Permeability
Coefficient for Ligand in DPPC so please help me.
--
Manoj Kumar Gadhwal (M. Pharma),
PhD Schloar,
Prin. K. M. Kundnani College of Ph
Hi,
I have generated a membrane protein complex and then added a waterbox using
Gromacs,but instead of being at the outer surfaces of lipid membrane,water
spreads all around the membrane. How to make appropriate water box?am I
doing a simple mistake?
Please help this beginn
manoj gadhwal wrote:
Dear friends,
I am using the GROMACS-4.5.3 for molecular dynamics as described
by* Justin Lemkul in Tutorial 2: KALP15 in DPPC. *I want to calculate
the Permeability Coefficient for Ligand in DPPC so please help me.
I briefly looked up this term and it sounds like you n
madhumita das wrote:
Hi,
I have generated a membrane protein complex and then added a waterbox
using Gromacs,but instead of being at the outer surfaces of lipid
membrane,water spreads all around the membrane. How to make appropriate
water box?am I doing a simple mistake?
If you've got wat
Hi,
While viewing a trajectory I am trying to see how a particular part or group
is behaving, while keeping the rest frozen (I dont want them to move). For
example, in a two domain protein keeping one domain frozen and seeing the
other domain movement or in a protein ligand complex keeing the prote
Ragothaman Yennamalli wrote:
Hi,
While viewing a trajectory I am trying to see how a particular part or
group is behaving, while keeping the rest frozen (I dont want them to
move). For example, in a two domain protein keeping one domain frozen
and seeing the other domain movement or in a pro
On 8/09/2011 3:55 AM, Justin A. Lemkul wrote:
Ragothaman Yennamalli wrote:
Hi,
While viewing a trajectory I am trying to see how a particular part
or group is behaving, while keeping the rest frozen (I dont want them
to move). For example, in a two domain protein keeping one domain
frozen a
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
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