Hi Justin,
Would you please tell me from the files I sent you which of them you
checked and how you got to the conclusion that (I mean which command )
This system behaves correctly - there is a zero interaction energy (both
Coulomb and LJ) at t=0, so it is fine.
Thanks
James
On Mon, Oct 20, 2014
On 10/20/14 8:11 AM, James Lord wrote:
Hi Justin,
Would you please tell me from the files I sent you which of them you
checked and how you got to the conclusion that (I mean which command )
This system behaves correctly - there is a zero interaction energy (both
Coulomb and LJ) at t=0, so it
Hi Justin,
Well, I tried clicking three different things that said download, but every
one of them tried to download software, spam, or charge me money, so I'm
going to assume that the files you sent me off-list are the same ones
you've posted here. If that's not the case, please find a better
: Thu, 16 Oct 2014 12:07:15 -0400
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to calculate protein-surface interaction
energy
Message-ID: 543fed33.5010...@vt.edu
Content-Type: text/plain; charset=windows-1252; format=flowed
On 10/16/14 11
On 10/18/14 6:45 AM, James Lord wrote:
Dear Justin Diogo,
Thanks for your comments, I did the steps you guys mentioned to calculate
protein-suface interaction energy and expect to see protein surface
option upon running g_energy but it is not the case, any comments? Here is
what I did,
gedit
Hi Justin,
Thanks for the prompt answer. I selected LJ-(SR) but I am getting a
positive fluctuating line over the simulation time. Looking at the vmd
movie I can see that protein (Lysozyme) is coming into contact with surface
afte 10ns and is 5 nm away at the beginning?? my surface is a not
On 10/18/14 8:51 AM, James Lord wrote:
Hi Justin,
Thanks for the prompt answer. I selected LJ-(SR) but I am getting a
positive fluctuating line over the simulation time. Looking at the vmd
movie I can see that protein (Lysozyme) is coming into contact with surface
afte 10ns and is 5 nm away at
Hi Justin,
1. Make sure your index groups are correctly constructed.
Do I need to use make ndx? I thought just adding energygrps=protein surface
at the end of .mdp is enough?
2. What does 5 nm correspond to? A COM distance? A minimum distance? If
the latter, then the LJ-SR energy should
On 10/18/14 9:30 AM, James Lord wrote:
Hi Justin,
1. Make sure your index groups are correctly constructed.
Do I need to use make ndx? I thought just adding energygrps=protein surface
at the end of .mdp is enough?
Surface isn't likely a default group (unless that's the name of the
You are right it is the name of molecule type in .top, and thus no error
upon executing grompp, so index group is constructed correctly right???
rvdw=1 nm so should be fine. and for the last part I agree.
Cheers
James
On Sun, Oct 19, 2014 at 2:34 AM, Justin Lemkul jalem...@vt.edu wrote:
On
On 10/18/14 9:55 AM, James Lord wrote:
You are right it is the name of molecule type in .top, and thus no error
upon executing grompp, so index group is constructed correctly right???
In theory, but if you're saying that at t=0, LJ-SR is not zero, something is
weird. Without access to your
Hi Justin,
Thanks, apparently I am doing some silly mistakes as I checked for another
system I have and ended up to the same problem. I am sending all the files
to your personal email and then if the problem is solved I will send a post
with description of the problem and the solution to the
On 10/18/14 8:41 PM, James Lord wrote:
Hi Justin,
Thanks, apparently I am doing some silly mistakes as I checked for another
system I have and ended up to the same problem. I am sending all the files
to your personal email and then if the problem is solved I will send a post
with description
, 16 Oct 2014 12:07:15 -0400
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to calculate protein-surface interaction
energy
Message-ID: 543fed33.5010...@vt.edu
Content-Type: text/plain; charset=windows-1252; format=flowed
On 10/16/14 11:42 AM
...@gromacs.org
Subject: Re: [gmx-users] How to calculate protein-surface interaction
energy
Message-ID: 543fed33.5010...@vt.edu
Content-Type: text/plain; charset=windows-1252; format=flowed
On 10/16/14 11:42 AM, James Lord wrote:
Hi Justin,
Sorry for not being clear, I have done
--
Date: Thu, 16 Oct 2014 12:07:15 -0400
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to calculate protein-surface interaction
energy
Message-ID
On 10/18/14 10:41 PM, James Lord wrote:
Hi Justin,
Here is the uploaded files on 4share.
http://www.4shared.com/folder/9CgRBgqp/_online.html
Well, I tried clicking three different things that said download, but every one
of them tried to download software, spam, or charge me money, so I'm
last.Diogo-- Date: Thu, 16 Oct 2014 12:07:15 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to calculate protein-surface interaction energy Message-ID: 543fed33.5010...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 10/1
--
Date: Thu, 16 Oct 2014 12:07:15 -0400
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to calculate protein-surface interaction
energy
Message-ID: 543fed33.5010...@vt.edu
Content-Type: text/plain; charset=windows-1252; format=flowed
Dear users,
I want to calculate the interaction energy (energy versus time) of a
protein (Lysozyme) adsorption process (20ns) on to a solid surface
(polyethylene).
when I use gmx energy -f md.edr -o energy.xvg and then selecting total
energy I end up with a messy graph!!! I am doing some wrong?
Hi Justin,
Thanks, the .mdp is the same as your tutorial for lysozyme, Can you explain
a bit more what to do? if I want to have total energy= vdw and
electrostatic?
Cheers
James
On Fri, Oct 17, 2014 at 12:51 AM, Justin Lemkul jalem...@vt.edu wrote:
On 10/16/14 5:46 AM, James Lord wrote:
On 10/16/14 10:47 AM, James Lord wrote:
Hi Justin,
Thanks, the .mdp is the same as your tutorial for lysozyme, Can you explain
a bit more what to do? if I want to have total energy= vdw and
electrostatic?
energygrps = Protein Surface
or whatever the names should be.
-Justin
--
Hi Justin,
Sorry for not being clear, I have done the simulation without specifying
the energygrps, so based on your previous comment I should use mdrun -rerun
trj.xtc -o energy.edr -pn index.ndx? and in index file define energygrps =
Protein Surface right?
If not appreciate if you give an
On 10/16/14 11:42 AM, James Lord wrote:
Hi Justin,
Sorry for not being clear, I have done the simulation without specifying
the energygrps, so based on your previous comment I should use mdrun -rerun
trj.xtc -o energy.edr -pn index.ndx? and in index file define energygrps =
Protein Surface
24 matches
Mail list logo
