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?
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?
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 md20ns.edr -o energy.xvg and then selecting total
energy I end up with a messy graph!!! Am I doing some thing
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
an example of the command with appropriate
input output etc.
Cheers
James
On Fri, Oct 17, 2014 at 3:49 AM, Justin Lemkul jalem...@vt.edu 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
: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 right
is a not charged
(polyethylene)?? I'd expect zero energy at beginning and upon touching the
surface negative value??? any comments? Sorry this has nothing to do with
Gromacs.
Cheers
James
On Sat, Oct 18, 2014 at 11:48 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/18/14 6:45 AM, James Lord wrote:
Dear
atom
Cheers
James
On Sun, Oct 19, 2014 at 2:05 AM, Justin Lemkul jalem...@vt.edu wrote:
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
/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
to the mailing list. Is
that fine with you?
Cheers
James
On Sun, Oct 19, 2014 at 4:26 AM, Justin Lemkul jalem...@vt.edu wrote:
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
...@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
Hi Justin,
Here is the uploaded files on 4share.
http://www.4shared.com/folder/9CgRBgqp/_online.html
Cheers
James
On Sun, Oct 19, 2014 at 2:23 PM, James Lord jjamesgreen...@gmail.com
wrote:
Hi Diogo,
Yes that is what I have at the end of top file.
ps: Sorry Justin I just saw your previous
you described before as being problematic.
Cheers
James
-Justin
On Sun, Oct 19, 2014 at 4:18 PM, Justin Lemkul jalem...@vt.edu wrote:
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
at 3:26 AM, Justin Lemkul jalem...@vt.edu wrote:
On 10/19/14 7:26 AM, James Lord wrote:
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
Dear users,
I have inserted a protein in a biphasic system (like Justin tutorial). My
question is if I want to sample different orientations of protein to one of
the phases how should I do that? I have rotated the protein with different
angles (90,180,270) around X,Y,Z axes but as I have
Dear Users,
I have a protein in a box and was wondering to know how to figure out the
protein distance to the box walls? I can see the box dimensions at the end
of .gro file but how to know what is (x,y,z) of protein in the box?? any
comments?
Cheers
James
--
Gromacs Users mailing list
* Please
Dear users,
I have MD of protein adsorption at an oil phase and am trying to calculate
the number of residues that contact the oil at each point in time? I have
tried
g_mindist -f mol.xtc -s md.tpr -on numcont.xvg
also with -group option but none of them gave what I am looking for. any
comments??
Dear users,
If I want to calculate distance of each residue's COM of a protein to a
surface is g_mindist going to be my friend? It is documented that
g_mindist computes the distance between one group and a number of other
groups. Both the minimum distance and the number of contacts within a given
anything?
Cheers
James
On Sat, Mar 28, 2015 at 1:17 AM, Justin Lemkul jalem...@vt.edu wrote:
On 3/27/15 8:03 AM, James Lord wrote:
Dear users,
If I want to calculate distance of each residue's COM of a protein to a
surface is g_mindist going to be my friend? It is documented
Hi Mahboobeh,
I recommend checking the created trajectories with gmx check.
Cheers
James
On Sun, Apr 26, 2015 at 12:39 AM, Ming Tang m21.t...@qut.edu.au wrote:
Hi，-e is end frame， -b is the start one.
Sent from my Huawei Mobile
Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote:
hi GMx
Dear gmx users,
I have a biphasic system, like Justin's tutorial, but I want to control
the protein to adsorb/desorb from the oil-water interface, I don't want the
protein to go through oil phase just want to keep it at the interface, I
have added a constant force at the end of the mdp file. i
...@vt.edu wrote:
On 5/2/15 10:02 AM, James Lord wrote:
Dear gmx users,
I have a biphasic system, like Justin's tutorial, but I want to control
the protein to adsorb/desorb from the oil-water interface, I don't want
the
protein to go through oil phase just want to keep it at the interface, I
Hi all,
How to calculate the area occupied by a protein in atomistic simulation (I
have performed the simulation already) but now want to calculate the area
occupied by the protein at two liquid interfaces and also interfacial free
energy reduction upon adsorption. Any detailed instructions is
Hi all,
I just installed a fresh ubuntu 14.04, and want to go ahead with
gromacs-5.0.4 installation, I am constantly getting this annoying message,
anyone can help?
root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
-- No compatible CUDA toolkit found
.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of James
Lord jjamesgreen...@gmail.com
Sent: 07 May 2015 14:05
To: gmx-us...@gromacs.org
Subject: [gmx-users] gromacs-5.0.4 installation problem
Hi
On Thu, May 7, 2015 at 7:45 PM, Roland Schulz rol...@utk.edu wrote:
Hi,
please rerun cmake from an empty build directly and post both the full
cmake output and the content of CMakeFiles/CMakeError.log.
Roland
On Thu, May 7, 2015 at 7:38 PM, James Lord jjamesgreen...@gmail.com
wrote:
Hi Mark
Dear gmx users,
pdb2gmx is complaining about Incomplete ring in HIS3, for 3V03.pdb
I saw Justin's comment
All structures have to be complete in order for pdb2gmx to process them.
The only atoms it can add are hydrogens. All heavy atoms are required. If
you place the missing atom(s) correctly,
Hi Justin,
I opened up the strucutre in Swissviewr. Then how can I have a pdb with
missing parts added?
Cheers
James
On Tuesday, May 5, 2015, Justin Lemkul jalem...@vt.edu wrote:
On 5/5/15 4:32 AM, James Lord wrote:
Dear gmx users,
pdb2gmx is complaining about Incomplete ring in HIS3
to
resolve this issue, any thought is greatly appreciated?
https://drive.google.com/file/d/0B0YMTXH1gmQsSWlXTU56R0FYcVk/view?usp=sharing
Cheers
James
On Sat, May 9, 2015 at 12:26 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/9/15 3:13 AM, James Lord wrote:
Hi Justin,
I opened up the strucutre
Thanks Justin.
On Wed, May 13, 2015 at 11:33 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/13/15 6:16 AM, James Lord wrote:
Many thanks Justin,
I created a new .pdb file with SwissPDBViewr but again executing pbd2gmx
is
giving the following warning and error
Warning: Starting residue
Dear gmx users,
I am trying to repeat Justin's Lysozyme tutorial for 1HFX.pdb,
https://drive.google.com/file/d/0B0YMTXH1gmQsUjVSd01ERXVpLTA/view?usp=sharing
I would like to know the total charge of my system but I have two statement
for that,after running
pdb2gmx -f 1HFX.pdb -o
I can see that I have two chains but can I simply say the total charge is
-7 e?
Cheers
James
On Thu, May 14, 2015 at 1:04 AM, James Lord jjamesgreen...@gmail.com
wrote:
Dear gmx users,
I am trying to repeat Justin's Lysozyme tutorial for 1HFX.pdb,
https://drive.google.com/file/d
/file/d/0B0YMTXH1gmQsMjlMTlNPeWJqdkk/view?usp=sharing
Thanks
James
On Fri, May 15, 2015 at 4:36 AM, Justin Lemkul jalem...@vt.edu wrote:
On 5/14/15 1:25 AM, James Lord wrote:
Hi all,
I am trying to neutralize this system (1HFX.gro) and genion is complaining
about solvent not being continuous
Thanks heaps mastermind Justin.
James
On Thursday, April 9, 2015, Justin Lemkul jalem...@vt.edu wrote:
On 4/9/15 2:45 AM, James Lord wrote:
Dear Users,
I am wondering if anyone can help me out with forced adsorption/
desorption
of a protein on surface. I am aware of pulling code
Dear Users,
I am wondering if anyone can help me out with forced adsorption/ desorption
of a protein on surface. I am aware of pulling code in Justin's tutorial
but that is not what I am looking for. I want a simple constant force
(perpendicular to the surface) method to push and/or pull the
Hi all,
I have a trivial question, What is the best box type and size for a big
protein such as BSA (attached .pdb) to minimize computational cost? what is
the rule of thumb re the protein distance to box wall?
This protein is around 16 nm in x direction and 6nm in y.
Hi Justin
For now I used
*mdrun -nt 1*
* and got rid of this error so hopefully the simulation wont crash. *
*Cheers*
*James*
On Sat, Jun 27, 2015 at 11:19 AM, James Lord jjamesgreen...@gmail.com
wrote:
Hi Justin,
I have asked this before, but this time I started up from scratch
://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing
Cheers
James
On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote:
On 5/16/15 11:35 PM, James Lord wrote:
Hi Justin
Thanks for this. Can you tell me which step(s) this bond length is
defined
What should I
, or even a
rhombic dodecahedron, which has a hexagonal base too.
Oh, and that structure of BSA is a dimer, while the biological unit is a
monomer...
Cheers,
Tsjerk
On Jun 27, 2015 7:20 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/27/15 2:38 AM, James Lord wrote:
Hi all,
I have
/27/15 7:46 PM, James Lord wrote:
Hi Justin Tsjerk,
Thanks for the info,
Tsjerk: I was looking for the monomer but could not find monomer structure
on protein data bank.
Because it crystallizes as a dimer. The state in the crystal is not
necessarily what one finds in solution. Just pull
Thanks heaps Justin
On Sun, Jun 28, 2015 at 1:58 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/27/15 9:48 PM, James Lord wrote:
Hi Justin,
Thanks for your email. Would you please tell me how I can do this? Sorry
to
bother you. below is the PBD I generated with Swiss-PdbViewr.
https
Hi All,
I have a system with 300k atoms, I don't have access to HPC facilities, Is
it possible to run gromcas on GPU on a desktop with following graphic card
for up to 200-300 ns?
00:02.0 VGA compatible controller: Intel Corporation 3rd Gen Core processor
Graphics Controller (rev 09)
01:00.0 VGA
Hi all,
I have made an oil slab (energy minimized, equilibrated nvt and npt), some
of the oil molecules are at the other end (periodicity).
https://drive.google.com/open?id=0B0YMTXH1gmQsYmdvQ3huYWtDaGs
then I decided to increase the box size in z direction a bit to make enough
room for protein,
Hi all,
I have a solvent filled in a box of dimensions 12 12 12 (solv_large.gro).
I want to adjust the density of system to 824 kg/m3. But I want editconf to
just change the volume only by changing the z direction ? is that possible?
I did
ediftconf -f solv_large.gro -o solv_large_scaled.gro
Hi Mohsen,
I am struggling with the same problem would you mind if I ask you to send
me your .mdp file ?
Cheers
James
On Tue, Aug 11, 2015 at 4:00 AM, Mohsen Ramezanpour
ramezanpour.moh...@gmail.com wrote:
As an update,
After reading the suggested links I tried two .mdp files which were
Hi Vikas,
typing mdrun or which mdrun in your terminal will tell you where it is
installed.
Cheers
James
On Monday, July 27, 2015, Live King vikasdubey1...@gmail.com wrote:
Hi Everyone,
I installed Gromacs-4.6.5 using the command sudo apt-get install gromacs,
then what is path of my Gromacs
Hi Justin,
Welcome back. Thanks I solved it the other day. I got the coordinate and
topology.
Cheers
James
On Monday, July 27, 2015, Justin Lemkul jalem...@vt.edu wrote:
On 7/24/15 4:16 AM, James Lord wrote:
Hi all,
I want to make the the hydrophobic layer Justin has made but only have one
Hi all,
I want to make the the hydrophobic layer Justin has made but only have one
.itp file from ATB for the hydrophobic layer (no topology and coordinate)?
Any suggestion where and how to start to make this hydrophobic layer? I am
aware of what Justin has suggested regarding using PRODRG
Hi all,
I am running energy minimization and grompp is complaining about following
error. I am using Gromacs version 4.6.3. On Gromacs website it is saying
that GROMOS96 54A7 files from ATB website were added to 4.6.2 and later
versions right?
Hi all,
I am running energy minimization and grompp is complaining about following
error. I am using Gromacs version 4.6.3. On Gromacs website it is saying
that GROMOS96 54A7 files from ATB website were added to 4.6.2 and later
versions right?
Hi all,
Sorry apparently my previous emails the shared links just contained one
file, apologize for that.
I am running energy minimization and grompp is complaining about following
error. I am using Gromacs version 4.6.3. On Gromacs website it is saying
that GROMOS96 54A7 files from ATB website
Hi all,
I am trying to figure out the number of hydrogen bonds between a protein
and membrane and which residues from protein were involved in hydrogen
bonding. I made an index file and selected the protein and membrane,
g_hbond -f md.xtc -s md.tpr -n index.ndx -num hbond.xvg -hbn hbond.ndx
Hi all,
I have a system with 300k atoms, but computationally it is expensive for me
doing simulation with such a big system, Is it possible to reduce the box
size? If yes how? (the .gro file is uploaded). I know from Justin tutorial
genconf
-nboxvector 1 1 1
Does the numbers after -nbox
Thanks Justin and Victor
On Sat, Jul 11, 2015 at 9:12 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/10/15 1:35 AM, James Lord wrote:
Hi all,
I have a system with 300k atoms, but computationally it is expensive for
me
doing simulation with such a big system, Is it possible to reduce
.
--
Szilárd
On Sat, Jul 4, 2015 at 1:40 PM, James Lord jjamesgreen...@gmail.com
javascript:; wrote:
Hi All,
I have a system with 300k atoms, I don't have access to HPC facilities,
Is
it possible to run gromcas on GPU on a desktop with following graphic
card
for up to 200-300 ns?
00:02.0 VGA
Hi all,
I have done two simulations following Justin's tutorial for biphasic
systems one with cyclohexane-water and the other one with a protein in
water phase that diffuses and comes to the cyclohexane-water interface at
some points and stays there for the rest of simulation. When I calculate
Hi Antonio,
Thanks for further information and the paper.
Cheers
James
On Thu, Sep 24, 2015 at 3:30 AM, Antonio Baptista <bapti...@itqb.unl.pt>
wrote:
> On Tue, 22 Sep 2015, Justin Lemkul wrote:
>
>
>>
>> On 9/21/15 10:22 PM, James Lord wrote:
>>
>>
Dear gmx users,
I want to use either gromos 43a2 or 54a7 in Gromacs to simulate protein
partitioning at biphasic liquid-liquid interfaces (Similar Justin's
tutorial for biphasic system). Which one is recommended if anyone has
experience with such system and why? appreciate any comments? I know
Hi all,
I sent this few days ago and I am still struggling with this, any
help,hints is highly appreciated.
-- Forwarded message --
From: James Lord <jjamesgreen...@gmail.com>
Date: Thu, Nov 26, 2015 at 11:18 PM
Subject: removing some atoms
To: "gmx-us...@gromacs.o
Hi all,
I have a oil slab and want to insert a protein so that almost half of the
protein is inserted into the oil and the other half is outside in the
vacuum. Is there any tools in Gromacs so that I can easily remove some of
the oil atoms and make a space for the protein insertion? My apology if
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