Yes.
The pow function is expensive though. The code will run much faster
if you can use rinvsix, such as check for 2*rinvsix c6/c12.
(I forgot the factor 2 in my previous mail).
Berk
From: makoto-yon...@aist.go.jp
To: gmx-users@gromacs.org
Date: Tue, 11 Jan 2011 10:10:56 +0900
Subject:
Dear all
I have the following system:
Two substrates (which are FCC lattices consisting of LJ particles) in a
distance of 50nm and between these substrates I put completely stretched
polymer chains. The substrates are parallel to xy plane and the chains are
vertical. The length of the stretched
On 2011-01-11 12.36, Simon Ágnes wrote:
Dear dr. van der Spoel,
I am wondering whether it is possible to perform molecular dynamics in
Gromacs with implicit membrane.
(I searched the mailing list archive and I guess that it is not
possible, but I would like to make sure, whether my information
Dear users, I have installed FFTW3 successfully, and confirmed its location
using locate:
/home/m/Desktop/gromacs-4.5.3/src/mdlib/gmx_fft_fftw3.c
/usr/lib/libfftw3.so.3
/usr/lib/libfftw3.so.3.2.4
/usr/lib/libfftw3_threads.so.3
/usr/lib/libfftw3_threads.so.3.2.4
/usr/lib/libfftw3f.so.3
Sergio Manzetti wrote:
Dear users, I have installed FFTW3 successfully, and confirmed its
location using locate:
/home/m/Desktop/gromacs-4.5.3/src/mdlib/gmx_fft_fftw3.c
/usr/lib/libfftw3.so.3
/usr/lib/libfftw3.so.3.2.4
/usr/lib/libfftw3_threads.so.3
/usr/lib/libfftw3_threads.so.3.2.4
Sergio Manzetti wrote:
Hi Justin, it was a blank ./configure
I don't know why a standard location like /usr/lib isn't be detected as
containing the libraries, but you can set LDFLAGS and CPPFLAGS accordingly so
that the libraries and headers are found. See the installation instructions
Thanks,
so LDFLAGS /home/user/gmx
and CPPFLAGS /home/user/gmx for example?
On Tue, Jan 11, 2011 at 2:19 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Sergio Manzetti wrote:
Hi Justin, it was a blank ./configure
I don't know why a standard location like /usr/lib isn't be detected as
On Tue, Jan 11, 2011 at 14:19, Justin A. Lemkul jalem...@vt.edu wrote:
Sergio Manzetti wrote:
Hi Justin, it was a blank ./configure
This defaults to something else than /usr/lib...
I don't know why a standard location like /usr/lib isn't be detected as
containing the libraries, but you
On Tue, Jan 11, 2011 at 07:00:46AM -0600, Sergio Manzetti wrote:
Dear users, I have installed FFTW3 successfully, and confirmed its location
using locate:
From your output I assume you did so via APT?
However, when I try installing Gromacs 4.5.3 the -/configure step yields:
configure:
On Tue, 11 Jan 2011 07:00:46 -0600
Sergio Manzetti sergio.manze...@vestforsk.no wrote:
Dear users, I have installed FFTW3 successfully, and confirmed its
location using locate:
However, when I try installing Gromacs 4.5.3 the -/configure step
yields:
configure: error: Cannot find
Thanks, doing # sudo apt-get install libfftw3-dev fixed the problem
Sergio
On Tue, Jan 11, 2011 at 7:31 AM, Jussi Lehtola jussi.leht...@helsinki.fiwrote:
On Tue, 11 Jan 2011 07:00:46 -0600
Sergio Manzetti sergio.manze...@vestforsk.no wrote:
Dear users, I have installed FFTW3 successfully,
Hi All,
I ran into a problem when running the methanol example in Getting Started.
When I ran grompp -v, I got the following:
Fatal error:
Atomtype CMET not found
I installed Gromacs 4.5.3 on Ubuntu and planned to learn the software. Now I
am stuck.
Many thanks for your help! I really
Mao Mao wrote:
Hi All,
I ran into a problem when running the methanol example in Getting
Started. When I ran grompp -v, I got the following:
Fatal error:
Atomtype CMET not found
I installed Gromacs 4.5.3 on Ubuntu and planned to learn the software.
Now I am stuck.
Many thanks for
Hi all,
This is my first time posting to the list, so please excuse any
ignorance on my part. I'm preparing a few test systems using Gromacs
4.5.3 with the ffamber96 forcefield. When I use gmxdump on the
resulting tprs, I see Proper Dihedrals but not RB Dihedrals. Does
ffamber96 use RB
Hi gmx-users,
I am trying to set up a simulation of a large protein in vacuo using the
OPLS-AA forcefield, with conditions based on Patriksson et. al (Biochemistry
2007, 46 p933). Basically after energy minimisation, the protein is run for
10ps in vacuum with constant temperature at 300K.
Hi all,
Is there a trick to analyze the temperatures of the atom groups if
they are not coupled separately? E.g. when the whole system is
T-coupled as the only group, can one determine the temperature
evolution for its parts?
Thank You.
=
Dr. Vitaly V. Chaban, Ph.D.
Hi,
While I understand that all non-bonded gmx potential shapes are intended
to be spherically symmetric, for a project of mine it would be helpful
to be able to have a non-bonded pair potential which is
geometry-dependent (that is, depending on the angle between 3 atoms).
Has anything
Thank you Angél and Stephane for your help
I also have another question. Using the pure hexane pdb (I am mixing
hexane and perfluorohexane), I've run simmulated annealing with a box of
500 molecules trying to obtain a good conformer distribution. The
heating steps were:
time (ps): 0 8 50
Hi Marcelo
1.- perfluorohexane is a quite rigid molecule so I wouldn't expect many
different conformations
2.- your simulation box is far away from the equilibrium
3.- you should inform about which force field and simulation conditions
are you using, for instance: was your simulation run at
I'm sorry to send another message but the sa.mdp file I sent was an old one
Best regards
From: jokle...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] perfluorohexane pdb... again
Date: Tue, 11 Jan 2011 17:44:50 +
Hello Angél,
I started with hexane just to know what
Hi,
I have two questions regarding the generalized born models implemented in
GROMACS.
1) Is it possible to perform an MD run using implicit solvent with an
united-atom force field? If so, how are determined the van der Walls radii
for H atoms?
2) How are determined the other van der walls
Vitaly Chaban wrote:
Hi all,
Is there a trick to analyze the temperatures of the atom groups if
they are not coupled separately? E.g. when the whole system is
T-coupled as the only group, can one determine the temperature
evolution for its parts?
You can use g_traj -ot, but as the help
Hi Marcelo
It is always good to see what happens to a known molecule before working
with your target with a new methodology. I took a closer look to your
pdb. You do have different hexane conformations. Anyway it is hard to
believe that your initial box was full of hexane... could you check
again
Dear all,
I am just a newbie to Gromacs so sorry for being naive with my
questions...
I would like to yield electron density profiles out of different
trajectories of membranes simulated with NAMD and last CHARMM forcefield
(all_36_lipid_cholesterol). I first tried to use pdb2gmx in order to
Hi!
Currently there is no support in Gromacs for implicit solvation using a
united-atom force field.
It is definitely possible though, but you need to consult the literature for
values for the radii.
For united-atoms, I guess the hydrogens you mention are the polar hydrogens?
All radii in the
Ramon Guixà wrote:
Dear all,
I am just a newbie to Gromacs so sorry for being naive with my questions...
I would like to yield electron density profiles out of different
trajectories of membranes simulated with NAMD and last CHARMM forcefield
(all_36_lipid_cholesterol). I first tried to
Justin,
Thanks for your response.
The membranes I've already run are made of POPC and cholesterol, so the
sphingomyelin membrane is my next simulation but I haven't managed to
find a proper forcefield for it. Would you know where to find this?
Ramon
-Original Message-
From: Justin A.
Angél,
I'm sending you my initial pdb in attachment. I chose the box size to
fit the experimental density.
I am just trying to get simple properties of the pure compounds hexane
and perfluorohexane and of a mixture 0.5 hexane/perfluorohexane (density
mainly). But maybe I just need a long
Ramon Guixà wrote:
Justin,
Thanks for your response.
The membranes I've already run are made of POPC and cholesterol, so the
sphingomyelin membrane is my next simulation but I haven't managed to
find a proper forcefield for it. Would you know where to find this?
Not for CHARMM, no, but
Hi All,
Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value of
the acidic hydrogen on the thiazolidinedione ring of pioglitazone is 4.57
(see attached Figure_1.gif). Therefore, the predominant species at pH 7.0
predicted by MarvinSketch is the one depicted in Figure_2.gif.
Hi Marcelo
your molecules are not in a box, the head of the pdb you sent to me is:
HEADER
TITLE Built with
Packmol
REMARK Packmol generated pdb file
REMARK Home-Page: http://www.ime.unicamp.br/~martinez/packmol
REMARK
ATOM 1 C1 HEX A
On 12/01/2011 8:11 AM, Nancy wrote:
Hi All,
Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value
of the acidic hydrogen on the thiazolidinedione ring of pioglitazone
is 4.57 (see attached Figure_1.gif). Therefore, the predominant
species at pH 7.0 predicted by MarvinSketch
On 12/01/2011 2:50 AM, RJ Nowling wrote:
Hi all,
This is my first time posting to the list, so please excuse any
ignorance on my part. I'm preparing a few test systems using Gromacs
4.5.3 with the ffamber96 forcefield. When I use gmxdump on the
resulting tprs, I see Proper Dihedrals but not
Hi Marcelo
your initial box is right, (4.72 nm)^3 = 105.15404e-27 m^3
500 hexane molecules = 500/(6.02e23)*86.16e-3 kg
the density of your initial system = 680.200377454 kg m^-3
The pdb file you sent contained two different structures (I just
realized about this) the first one is in a box of the
On 12/01/2011 2:29 AM, Zoe Hall wrote:
Hi gmx-users,
I am trying to set up a simulation of a large protein /in vacuo/ using
the OPLS-AA forcefield, with conditions based on Patriksson et. al
(Biochemistry 2007, 46 p933). Basically after energy minimisation,
the protein is run for 10ps in
Thanks again Justin
-Original Message-
From: Justin A. Lemkul jalem...@vt.edu
Reply-to: jalem...@vt.edu jalem...@vt.edu, Discussion list for
GROMACS users gmx-users@gromacs.org
To: Gromacs Users' List gmx-users@gromacs.org
Subject: Re: [gmx-users] g_density CHARMM
Date: Tue, 11 Jan 2011
Dear Gromacs users,
I'm sure that the Gromos5A36 force field have topology to the heme
group and would like to know how to proceed to perform a successfull MD
simulation on a protein with this group. Should I just write the name of
the heme topology file inside the protein.top file
Tanos Franca wrote:
Dear Gromacs users,
I'm sure that the Gromos5A36 force field have topology to the heme
group and would like to know how to proceed to perform a successfull MD
simulation on a protein with this group. Should I just write the name of
the heme topology file inside
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