Hi Johnny,
I am not familiar with pulling and even less with gromacs but I would be
very cautious in using the MARTINI force field for the kind of
simulation
you are doing.
This CG model has not been tested at all for this and it might not be
very good at it! But I would be very interested
Dear all,
I am a bit confused about how the pair potentials (PPs)are calculated.
If I state explicitly sigma and epsilon values for the pair potentials,
can I then still have a coulomb scaling of my 1-4 interactions?
Say I set gen-pairs to yes, although I have all possible pair
potential
Hi,
The charges are always scaled with fudgeQQ.
For the LJ parameters the precendence is:
For an atom pair in the [ pairs ] section with type A and B:
if parameters are present on the line in the [ pairs ] section use those,
otherwise
if parameters are present in the [ pairtypes ] section use
Dear all,
i
want to install mdrun_make_hole in my home directory(/home/cm/install).
For that the steps i have followed are..
1) installation of fftw
cd /home/cm/install
cp fftw-3.2.1.tar.tar ../
tar -zxvf fftw-3.2.1.tar.tar
cd fftw-3.2.1.
./configure --enable-float
Hi Berk,
Thanks for your answer, I am happy to have the priority list for how the
van der Waals term of the pair potential is calculated.
About fudgeQQ, do you mean that the pair potentials' coulomb terms are
scaled with the fudgeQQ value, even when gen-pairs is set to no?
( I see from the
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least qualitatively
they behave quite reasonably, although these models have never been
parameterized or systematically tested with this kind of
--
Message: 1
Date: Wed, 29 Jul 2009 16:04:54 -0700 (PDT)
From: Johnny Lam john...@berkeley.edu
Subject: [gmx-users] Pulling a CG protein
To: gmx-users@gromacs.org
Message-ID:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least qualitatively
they behave quite reasonably, although these models have never been
parameterized or systematically tested with
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least
qualitatively
they behave quite reasonably, although these
Dear Ansgar Esztermann,
Thanks for your reply. I have source .bashrc after adding the
environment variables as follows..
source .bashrc and then run
./configure --enable-float --prefix=/home/cm/install --program-suffix=_h
The same problem arise again.
Looking for ur
XAvier Periole wrote:
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least qualitatively
they behave quite reasonably,
Hello everybody
I am a Gromacs beginner and I am trying to simulate an infinite graphene
lattice (see 07.29.09 posts - I don't know how to reply directly to
posts, can someone tell me how to do that?). Mark suggested having a
look at http://www.gromacs.org/WIKI-import/Carbon_Nanotube . I had
On Jul 30, 2009, at 12:10 PM, David van der Spoel wrote:
XAvier Periole wrote:
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point
out
that we have used CG models to pull on
Hi,
FudgeQQ is always used, independently of gen-pairs.
I have added a note about this in the manual.
Berk
Subject: RE: [gmx-users] generate pair list and 1-4 interactions
Date: Thu, 30 Jul 2009 17:07:49 +0800
From: ch...@nus.edu.sg
To: gmx-users@gromacs.org
Hi Berk,
Thanks
Hi,
Just picking up the following bits of the conversation:
David van der Spoel wrote:
What does this boil down to? If you want to apply MD tools to get
an accurate force curve *now*, use all atom models. [..]
x.peri...@rug.nl said:
This is of course the idea, but then comes the problem of
Hi,
What's the version of your gromacs?
~ Vitaly
I am a Gromacs beginner and I am trying to simulate an infinite graphene
lattice (see 07.29.09 posts - I don't know how to reply directly to
posts, can someone tell me how to do that?). Mark suggested having a
look at
Giulio,
I suggest you to try x2top which is spread with gromacs-3.3.1. The
newer versions of x2top are not sain.
Vitaly
On Thu, Jul 30, 2009 at 1:48 PM, Giulio Scocchigiulio.scoc...@icimsi.ch wrote:
Hi Vitaly
Well, I have downloaded it just a couple of months ago, so I guess it should
be
You may also find a number of the already generated CNT topologies on
the gromacs site uploaded by me for different systems containing CNTs
to see how it should look like.
On Thu, Jul 30, 2009 at 1:48 PM, Giulio Scocchigiulio.scoc...@icimsi.ch wrote:
Hi Vitaly
Well, I have downloaded it just a
Vasilii,
Telling the truth, I don't already remember what was wrong with CNT
topology generation from the coordinate file but I didn't succeed with
any version starting from 3.3.3. So I still keep x2top (3.3.1) for the
CNTs.
There was also several reports in gmx-list that x2top(4.0.X) behaves
Giulio,
Look here:
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies
It seems some ones were missed as migrating from the old site. I will
send you more topologies attached to the next email.
Moreover, how can I reply directly to a post in
If you unzipped/untarred the archive properly it should be some system
already prepared to run. So you can just start grompp and mdrun to
begin MD.
By the way, I had already seen that web page... I downloaded and unzipped the
swcnt file, but I can't understand what kind of file it is.
Dear Justin,
i am trying to insert a peptide in trans-bialyer orientation
into a pre-equilibrated POPC bilayer using inflategro script. After 13 steps
of compression, the area per lipid is 2.61956768363491 nm^2, whereas the
desired area per lipid is 0.658 nm^2. But when i try
Hi Mark,
Sorry to trouble you again!
I made two tests, by using one-processor and one 32-processors on the
same cluster. I used 4000SPC/E waters (OPLS-AA ff.) The former
(one-processor) gives the exactly the same potential. However, the
latter still shown some deviation of the potential. When I
Moutusi Manna wrote:
Dear Justin,
i am trying to insert a peptide in trans-bialyer
orientation into a pre-equilibrated POPC bilayer using *inflategro*
http://moose.bio.ucalgary.ca/files/inflategro script. After 13 steps
of compression, the area per lipid is
Hi,
Your command line is incorrect.
-reprod should be used without yes.
-reprod is yes
-noreprod is no
mdrun -cpi has no effect on your results at all.
But always remember that MD is chaotic, there is no point in trying
to reproduce trajectories exactly, unless for a very special purpose.
Berk
Baofu Qiao wrote:
Hi Berk,
Thanks for pointing out my mistake!
What I worry about is how big the deviation is after several continuations? If
it is unpredictable, it is a sad news.
The objective is to avoid perturbing the system *with the restart*. Any
perturbation will make the trajectory
Hi ,
I am having some problems when running in parallel. Although my jobs
run to completion I am getting some worrying domain decomposition
statistics in particular the average load imbalance and the
performance loss due to load imbalance see below:
D O M A I N D E C O M P O S I T I O
Hi XAvier, Marc, and David,
Thank you so much for the reply and encouragement ;-). Please forgive me
as I am trying to learn how to reply to the thread that I started. With
regards to the fun discussion, it was my original intent to compare the
results of pulling with the MARTINI forcefield (if
Hi,
Since in graphene, C is sp2 hybridized with covalent radius as 0.073 nm, how
come C-C bond length =0.142 nm which is less that twice the covalent radius,
does this mean 2 C's overlap (which is unphysical). The source of my data is
wikipedia.
Also, there is no bare C in GROMOS96 53a6 ff,
Manik Mayur wrote:
Hi,
Since in graphene, C is sp2 hybridized with covalent radius as 0.073 nm,
how come C-C bond length =0.142 nm which is less that twice the covalent
radius, does this mean 2 C's overlap (which is unphysical). The source
of my data is wikipedia.
Wikipedia will also
Hi,
I've been trying for days to try to figure out how to configure GROMACS
for mixed QM/MM modeling, and it is a nightmare. The only manuals in
existence seem to give less than half the story, and I have no
experience with this kind of program.
I have managed to do ./configure
Hello,
I have generated several trajectory files (*.trr, *.xtc) from running MD
simulations, and I can view them with the ngmx program included with
GROMACS, but I am unable to view them in Visual Molecular Dynamics (VMD).
Please advise.
Thanks,
Nancy
Hi Nancy,
Is it loading it in, but not displaying it? If that's the case, you
need to load a pdb file in first or else VMD can't guess how to
display the molecule from position data only. If that's not the
problem, then you're going to have to give more information than just
that it
Thanks, it works.
Nancy
On Thu, Jul 30, 2009 at 7:12 PM, Joshua Adelman jadel...@berkeley.eduwrote:
Hi Nancy,
Is it loading it in, but not displaying it? If that's the case, you need to
load a pdb file in first or else VMD can't guess how to display the molecule
from position data only.
Jennifer Williams wrote:
Hi ,
I am having some problems when running in parallel. Although my jobs run
to completion I am getting some worrying domain decomposition statistics
in particular the average load imbalance and the performance loss due to
load imbalance see below:
Please report
Mark Abraham wrote:
Jennifer Williams wrote:
Hi ,
I am having some problems when running in parallel. Although my jobs
run to completion I am getting some worrying domain decomposition
statistics in particular the average load imbalance and the
performance loss due to load imbalance see
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