Dear All,
I am trying to simulate water flow in CNT and just followed the website:
http://cs86.com/CNSE/SWNT.htm
I did the following:
1. ffgmx.n2t
must change this files name to ffencadv.n2t and add the following 2 lines:
C C 1 C ; CNT Carbon with one bond
C C 2 C C ; CNT double bonded
Thank you for your kind response.
I think that I do not clearly describe the system.
The loop I mentioned above seems to interact with the other parts of the
protein with hydrophobic interactions.
So, the displacement of the loop from the original position will make the
free energy difference,
Now, did you try searching the mailing lists before asking this? This
question pops up once a week or so. Check the archives: the truth is out
there.
/Erik
Dechang Li skrev:
Message: 2
Date: Mon, 21 Apr 2008 10:43:27 -0400
From: Jian Zou [EMAIL PROTECTED]
Subject: [gmx-users] Re: the number
Wei, Xiupeng wrote:
Hi Mark,
Could you give me some suggestions for how to put two boxes
contacting each other? Thanks.
Best regards,
xiupeng
Dear Vasilii and other users,
Thanks for you reply.
I triedto do the simulation you said. But how to setup the initial
I think you'll have to do it manually. The geometry for ice shouldn't be
too hard to find, and with that you can build your own coordinate file
for a chunk of ice. Ice is not the only nucleating agent for water
freezing though. In large scale nucleation protocols some silver
compound is used
SeungPyo Hong wrote:
Thank you for your kind response.
I think that I do not clearly describe the system.
The loop I mentioned above seems to interact with the other parts of the
protein with hydrophobic interactions.
So, the displacement of the loop from the original position will make
the
There are several different crystal phases of water. For simulation
setup, it's best (always, not only with freezing of water) to check the
literature. This will also give you a hint on what have already been
done. Quite a few MD simulations of ice were reported. If you have a
good idea on what
On Mon, Apr 21, 2008 at 07:09:31PM +0400, Vasilii Artyukhov wrote:
Dear GROMACS users,
particularly, those experienced with membrane simulations,
I want to simulate lipid bilayers (e.g., DPPC) in the presence of certain
small solutes, much like what was done in A.K. Sum J.J. de Pablo,
Hero wrote:
Dear All,
I am trying to simulate water flow in CNT and just followed the website:
http://cs86.com/CNSE/SWNT.htm
I did the following:
1. ffgmx.n2t
must change this files name to ffencadv.n2t and add the following 2 lines:
C C 1 C ; CNT Carbon with one bond
C C 2 C C ; CNT
Hello all.
I'm trying to simulate an argon liquid. The OPLS-AA force field is used
with the files from /usr/local/gromacs/share/gromacs/top. But I get an
error when I run
$ grompp -f NVT.mdp -c Ar.gro -p Ar.top
---
Program grompp, VERSION
Just thinking out loud, but maybe Argon is too long of a name for the
residues. The longest I think I've seen is 4 characters (something like LYSH
or ARGN, for example). Maybe the length of the name is throwing off the
formatting. Why don't you try again with a residue name of something like
set sel [atomselect $molid selection]
for {set iframe 0} {$iframe $nframe} {incr iframe} {
$sel frame $iframe
$sel update
$sel get {the property you want}
}
you may go to vmd mailing list for more details.
Message: 1
Date: Tue, 22 Apr 2008 10:42:56 +0800
From: Dechang Li
Justin A. Lemkul skrev:
Just thinking out loud, but maybe Argon is too long of a name for the
residues. The longest I think I've seen is 4 characters (something like LYSH
or ARGN, for example). Maybe the length of the name is throwing off the
formatting. Why don't you try again with a residue
Hi,
Your formatting is incorrect.
The .gro format is a very old GROMOS fixed format (not free format).
See the manual for the details:
http://www.gromacs.org/documentation/reference/online/gro.html
Berk.
Date: Tue, 22 Apr 2008 12:12:17 +0200
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Berk Hess wrote:
Hi,
Your formatting is incorrect.
The .gro format is a very old GROMOS fixed format (not free format).
See the manual for the details:
http://www.gromacs.org/documentation/reference/online/gro.html
Thanks for the link - I remember asking for it on this list years ago :-)
Dear Gromacs,
Actually, the error is for all the 144 atoms on SWNT_6_6_144:
when I ran:
x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp
Error message appeared:
Can not find forcefield for atom C-1 with 2 bonds
.
Can not find forcefield for atom C-143 with 2 bonds
Can not
Hero wrote:
Dear Gromacs,
Actually, the error is for all the 144 atoms on SWNT_6_6_144:
when I ran:
x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp
Error message appeared:
Can not find forcefield for atom C-1 with 2 bonds
.
Can not find forcefield for atom C-143 with 2
Hello,
I have a problem about genbox command in GMX. I'm running genbox to randamly
insert molecules. Because the probobility of successful insertion is low, I
have to use a large number for the -try variable. After running genbox I
found sometimes the memory cost increased gradually after
Hello,
I am simulating a trimer in a membrane. In one of my simulation two of the
monomers are on one side of the box and the other monomer is on the other
side of the box. I tried using trjconv to center the whole thing in the
center of my simulation cell but have failed miserably. I also
On Tue, 22 Apr 2008 14:14:19 -0700
Ilya Chorny [EMAIL PROTECTED] wrote:
Hello,
I am simulating a trimer in a membrane. In one of my simulation two of the
monomers are on one side of the box and the other monomer is on the other
side of the box. I tried using trjconv to center the whole thing
Just to clarify.
I would run
trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro?
What would I run next?
Thanks,
Ilya
On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole [EMAIL PROTECTED] wrote:
On Tue, 22 Apr 2008 14:14:19 -0700
Ilya Chorny [EMAIL PROTECTED] wrote:
Hello,
I am
So I got it to center my protein (using -pbc nojump) and keep the trimer
and the membrane in tact but it completely destroyed my water. I was hoping
I could get the whole simulation box back with the protein in the center.
Is that possible?
Thanks,
Ilya
On Tue, Apr 22, 2008 at 3:25 PM, Ilya
I've often found it necessary to do multiple trjconv steps to get the result I
want. So in this case, I'd probably make sure my protein is genuinely centered
in the box, then take that output .xtc and then make sure everything is whole
and approximately in the box (-pbc whole).
-
Thank you very much Mark~
On Tue, Apr 22, 2008 at 4:27 PM, Mark Abraham [EMAIL PROTECTED]
wrote:
SeungPyo Hong wrote:
Thank you for your kind response.
I think that I do not clearly describe the system.
The loop I mentioned above seems to interact with the other parts of the
I have put together this general response to the vast amounts of e-mails I
have been receiving as of late in regards to how to use GROMACS to model
carbon nanotubes.
New GROMACS Users
First if you are new to GROMACS step on before you even install the
So I got it to work for my trimer by doing the following.
1.) trjconv -f *.xtc -s *.tpr -pbc nojump -o out.xtc
2.) trjconv -f out.xtc -s *.tpr -pbc mol -center -boxcenter rect
The first step unwraps the whole trajectory and the second step wraps it
back up.
Cheers,
Ilya
--
Ilya Chorny Ph.D.
Additionally if some one would like to put this on GROMACS's wiki please
feel free to do so, I would but with graduation coming up I don't even
have
time to be writing this. If you would like the files I have on my site
those
can be provided for this purpose as well!
Wikified here
Hi,
Sorry for not replying immediately.
Gromacs ver 3.2.1
OS is Red hat enterprise 4
Initially I had tried reading the file from an external hard disk and now I
copied it to another system and tried again. Still the same error.
The reason why I was truncating was due to a magic number error I
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