Hi Gromacs users,
Am running a MD simulation over a protein complex and before adding the
ions. we run a grompp option then we get result as model net charge as some
integer ie if +2.00. so we got to add 2 CL ions. But when i ran my protein
for grompp it didnt give me any net charge so am not
On 7/09/2011 4:14 PM, aiswarya pawar wrote:
Hi Gromacs users,
Am running a MD simulation over a protein complex and before adding
the ions. we run a grompp option then we get result as model net
charge as some integer ie if +2.00. so we got to add 2 CL ions. But
when i ran my protein for
On 7/09/2011 1:01 PM, Nathalia Garces wrote:
Hello,
The last 6 months I've been working with gromacs (4.5.3 and 4.5.4) in
Ubuntu (10.4) and it has worked fine. The problem started when I
changed the linux distribution to Scientific Linux (5.3)... I followed
the same steps to
Message: 4
Date: Tue, 06 Sep 2011 22:35:09 +1000
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] atom type OXT
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4e66137d.9040...@anu.edu.au
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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
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
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
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 am
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:
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 currently
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
Message: 1
Date: Wed, 07 Sep 2011 12:01:00 +0200
From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de
Subject: Antw: Re: Antw: Re: Re: [gmx-users] constant PH simulations
To: gmx-users@gromacs.org
Message-ID: 4e675cfc02f100014...@gwsmtp1.uni-regensburg.de
Content-Type:
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
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
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
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
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
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
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
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
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