Okay, thanks, I'll try longer simulations.
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Fri, April 22, 2011 5:18:50 PM
Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation
majid hasan wrote
Dear All,
I am doing a MD simulation of dna, and cnt in water. I get a stable simulation
in which DNA, and CNT wiggles around there positions, but they don't seem to be
attracted towards each other. CNT starts in the middle of the box and just
moves
a little, and DNA starts at top right
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Fri, April 22, 2011 1:51:47 AM
Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation
On 4/22/2011 6:48 PM, Mark Abraham wrote:
On 4/22/2011 4:54 PM, majid hasan wrote:
Dear All,
I am doing a MD simulation
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Fri, April 22, 2011 10:44:45 AM
Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation
majid hasan wrote:
I just checked and DNA position should
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Fri, April 22, 2011 10:59:22 AM
Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation
majid hasan wrote:
Yes, ideally I didn't want to, but I read somewhere on mailing list
@gromacs.org
Sent: Thu, April 21, 2011 4:02:57 AM
Subject: Re: [gmx-users] dna and cnt get distorted in md simulation
majid hasan wrote:
Dear All,
I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then
ran the mdrun with integrator = md. I am using a small ssDNA consisting of two
majid hasan wrote:
first .mdp file is the original one, and modified .mdp is the one where I
made
modifications, and I have tried both, and both lead to stable structures for
individual molecules, and distorted structures for combined system.
The reason I asked is that the two are very
: Re: [gmx-users] dna and cnt get distorted in md simulation
majid hasan wrote:
Okay, so here is the file that I used for both energy minimization (with
integrator = l-bfgs), and MD (integrator = md). Everything other than the
value
of integrator was same for both energy minimization and MD
Dear All,
I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure
it
works) using l-bfgs integrator. When I run in the .trr output file, ends of dna
only move slightly towards cnt, but it doesn't wrap around it. Could anyone
please guide me what can be the possible
cnt
majid hasan wrote:
Dear All,
I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure
it works) using l-bfgs integrator. When I run in the .trr output file, ends of
dna only move slightly towards cnt, but it doesn't wrap around it. Could
anyone
please guide me
Okay, thanks a lot.
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Wed, April 20, 2011 12:01:33 PM
Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of
dna around cnt
majid hasan
Dear All,
I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then
ran
the mdrun with integrator = md. I am using a small ssDNA consisting of two
residues only (66 atoms), and a small CNT of about 80 atoms.
My commands are:
For energy minimization,
grompp -f lbfgs.mdp
Dear All,
In an attempt to create CNT topology with g_x2top and amber99, I was getting
this error: no or incorrect atomname2type.n2t file found. So I tried to create
a
atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form:
UNNAMED
400
1TUB CA1 0.392
users gmx-users@gromacs.org
Sent: Tue, April 19, 2011 10:40:53 AM
Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99
majid hasan wrote:
Dear All,
In an attempt to create CNT topology with g_x2top and amber99, I was getting
this error: no or incorrect atomname2type.n2t file found
A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, April 19, 2011 10:40:53 AM
Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99
majid hasan wrote:
Dear All,
In an attempt to create CNT topology with g_x2top and amber99, I was getting
A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Tue, April 19, 2011 11:47:44 AM
Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99
majid hasan wrote:
Just a little addition to my previous reply: if I run the same procedure with
oplsaa, it works. Now
Yea, sure, thanks.
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Tue, April 19, 2011 12:09:06 PM
Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99
majid hasan wrote:
Actually, I just
Dear All,
I am doing a DNA-CNT simulation, and I am trying to generate a topology of CNT
using Amber99, which has been used for such systems, and CNT atoms are modeled
using sp2 carbon parameters.
But when I try to create topology file using: pdb2gmx -f cnt.pdb -p cnt.top,
and
Amber99
,
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Mon, April 18, 2011 10:25:39 AM
Subject: Re: [gmx-users] Simulation of CNT with Amber forcefield
majid hasan wrote:
Dear All,
I am doing a DNA
?
Thanks a lot,
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Sun, April 17, 2011 4:39:56 AM
Subject: Re: [gmx-users] genbox output taking forever to complete
majid hasan wrote:
Okay, so I divided
Okay, thank you.
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Sun, April 17, 2011 12:28:47 PM
Subject: Re: [gmx-users] genbox output taking forever to complete
majid hasan wrote:
Okay, so here is an output
Alright, thanks.
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Sun, April 17, 2011 12:31:49 PM
Subject: Re: [gmx-users] genbox output taking forever to complete
majid hasan wrote:
Okay, so here is an output
Dear All,
I want to simulate DNA-CNT interaction, and reproduce the helical wrapping of
DNA around CNT in the first step, and later study the effects of temperature,
CNT length etc on the favorable geometries of hybrid.
I have created .top files for DNA, and CNT separately. To generate the top
@gromacs.org
Sent: Sun, April 17, 2011 4:54:11 PM
Subject: Re: [gmx-users] .top file for DNA-CNT
majid hasan wrote:
Dear All,
I want to simulate DNA-CNT interaction, and reproduce the helical wrapping of
DNA around CNT in the first step, and later study the effects of temperature,
CNT length etc
Okay, thanks, I'll stick to Amber then.
Thanks again,
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Sun, April 17, 2011 6:35:07 PM
Subject: Re: [gmx-users] .top file for DNA-CNT
majid hasan wrote:
Okay, so
Dear All,
I am trying to add a single strand dna, and single walled carbon nanotube in a
box using the genbox command. After typing following command:
genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o
cntdna.gro,
I get: Reading solute configuration
Containing
Okay, thanks Justin!.
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Sat, April 16, 2011 6:19:39 PM
Subject: Re: [gmx-users] genbox output taking forever to complete
Justin A. Lemkul wrote:
majid hasan
Subject: Re: [gmx-users] genbox output taking forever to complete
Justin A. Lemkul wrote:
majid hasan wrote:
Dear All,
I am trying to add a single strand dna, and single walled carbon nanotube in
a
box using the genbox command. After typing following command:
genbox -cp
Okay, thank you. I'll try to fix it.
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Sun, April 10, 2011 4:17:59 AM
Subject: Re: [gmx-users] Dangling bond error for dna
majid hasan wrote:
Sorry, the pdb file
jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Sun, April 10, 2011 4:17:59 AM
Subject: Re: [gmx-users] Dangling bond error for dna
majid hasan wrote:
Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted
below.
Output of pdb2gmx is attached.
You have
Okay, I am trying AmberTools as well. Thanks Justin!
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Sun, April 10, 2011 10:16:57 AM
Subject: Re: [gmx-users] Dangling bond error for dna
majid hasan wrote
Okay, thanks a lot.
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Sat, April 9, 2011 3:05:48 PM
Subject: Re: [gmx-users] Naming of DNA residues, and structure of .pdb file
majid hasan wrote
Dear All,
I created .pdb file for dna using gabedit. But when I try to create the
topology
file I get this error: Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb
file.
: Sat, April 9, 2011 7:18:30 PM
Subject: Re: [gmx-users] Dangling bond error for dna
majid hasan wrote:
Dear All,
I created .pdb file for dna using gabedit. But when I try to create the
topology file I get this error: Fatal error:
There is a dangling bond at at least one of the terminal ends
Dear All,
I am trying to simulate the interaction between DNA, and CNT. But when I try to
create the toplogy file with command
g_x2top -f ssdna.gro -o ssdna.top -ff select, I get the following error: Fatal
error: Could only find a forcefield type for 119 out of 287 atoms
I am using the
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Fri, April 8, 2011 12:54:38 PM
Subject: Re: [gmx-users] .n2t file for ssDNA
majid hasan wrote:
Dear All,
I am trying to simulate the interaction between DNA, and CNT. But when I try
, 2011 3:03:23 PM
Subject: Re: [gmx-users] .n2t file for ssDNA
majid hasan wrote:
Thanks Justin!
But with pdb2gmx, after selecting force field and water model, I get this
error: Fatal Error: Residue 'DA3' not found in residue topology (on selecting
oplsaa), and when I selected amber99, I got
: Fri, April 8, 2011 3:14:47 PM
Subject: Re: [gmx-users] .n2t file for ssDNA
majid hasan wrote:
Okay, I'll try to create a better .pdb file, and see how it goes. So if
oplsaa
doesn't have nucleic acids, then Amber is a better choice?
A force field should be chosen based on thorough study
Dear All,
I want to simulate interaction between single strand dna and cnt. I tried to
use
Biomer (from case group webpage), but it's not working. When I try to open
B.html in my browser, I get a blank page. Could anyone please tell me if there
is another way to generate .pbd file for dna?
for GROMACS users gmx-users@gromacs.org
Sent: Mon, February 14, 2011 9:39:12 PM
Subject: Re: [gmx-users] Gromacs Installation
On 15/02/2011 4:35 PM, majid hasan wrote:
Okay, I'll do this. I have also realized after browsing through
config.log, that Xlib.h is absent. Where do I get
Dear All,
I am trying to install gromacs in ubuntu. I configured both fftw and gromacs in
my home folder following the instructions on
http://www.gromacs.org/Downloads/Installation_Instructions. However, when I do
make, I get an error in the end (pasted below). I have also attached the log
it into
repository.
There maybe also some other ways.
HTH,
lina
On Tue, Feb 15, 2011 at 6:23 AM, majid hasan pu_majidha...@yahoo.com wrote:
Dear All,
I am trying to install gromacs in ubuntu. I configured both fftw and gromacs
in
my home folder following the instructions on
http
,
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Mon, February 14, 2011 6:46:47 PM
Subject: Re: [gmx-users] Gromacs Installation
majid hasan wrote:
Okay, I'll try with --enable-single. But as far
Okay. Actually, second time, I over-worte the first installation. I mean I
didn't uninstall the first one, I just ran the whole process again starting
from
fftw$./configure. I am not sure if that is all right, I just did it to find out
the problem. In the third attempt (without issuing
: Mon, February 14, 2011 9:07:15 PM
Subject: Re: [gmx-users] Gromacs Installation
clean reinstallation.
make uninstall
make distclean
rm -r the untar one
from source re-install it again.
lina
On Tue, Feb 15, 2011 at 12:39 PM, majid hasan pu_majidha...@yahoo.com wrote:
Okay. Actually, second time
I have attached the output of demo, and another Okay, I just ran the demo and
kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here
is what I got.
You seem to have the DISPLAY variable is set, so we will pop up a window with
the output of the pdb2gmx program
Press
I have attached the output of demo, and water with the message.
I just ran the demo and kept pressing enter whenever it asked me. Demo ran the
pdb2gmx first, and here is what I got.
You seem to have the DISPLAY variable is set, so we will pop up a window with
the output of the pdb2gmx
] Output of Gromacs Demo
majid hasan wrote:
I have attached the output of demo, and another Okay, I just ran the demo and
kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here
is what I got.
You seem to have the DISPLAY variable is set, so we will pop up a window
Okay, thanks. I will install it again in some other directory.
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Sun, February 13, 2011 1:39:16 PM
Subject: Re: [gmx-users] Output of Gromacs Demo
majid hasan
Dear All,
I installed the gromacs on Ubuntu, and ran the demo. But every time it produces
an output file, I get this error: output.pdb2gmx: Permission denied., so I
can't view the output. I am also unable to locate the .trr file, which is
supposed to be the ultimate output of demo. Could
Dear All,
I installed gromacs-4.5.3 using cygwin on windows 7, following the instructions
on http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO.
However, after installation, when I tried to run gromacs, I couldn't find the
share folder in D:/cygwin/usr/local/gromacs. This
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