You can build it using VMD (VIsual Molecular Dynamics)
2011/5/30 albert leu...@yeah.net
Dear all:
I would like to use charmm36 and POPC for membrane protein simulation.
and I am wondering where can I download charmm36 pre-pribriumed POPC PDB and
topol file for gromacs?
Thank you very
Hello, does anybody have an idea if there are availbale PDB files which
represent metal surfaces for transition state metals, to be used for MD?
BW
S
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Thank you
On Thu, Apr 28, 2011 at 6:26 PM, Ran Friedman ran.fried...@lnu.se wrote:
Hi,
That's unlikely, but maybe the following publications can help you to build
the surface:
@Article{Iori2008,
author = Iori, F and Corni, S,
title = {Including image charge effects in the molecular
Hello everyone, is this citation proper for citing NICS?
I.I. Rabi, J.R. Zacharias, S. Millman, P. Kusch (1938). A New Method of
Measuring Nuclear Magnetic Moment. *Physical
Reviewhttp://en.wikipedia.org/wiki/Physical_Review
* *53*: 318. doi http://en.wikipedia.org/wiki/Digital_object_identifier:
Beacuse I want to cite NICS.
On Fri, Mar 25, 2011 at 8:56 PM, Emanuel Peter
emanuel.pe...@chemie.uni-regensburg.de wrote:
Hello,
Why do you ask this ?
Sergio Manzetti 25.03.11 13.09 Uhr
Hello everyone, is this citation proper for citing NICS?
I.I. Rabi, J.R. Zacharias, S. Millman
Hello, I am doing a refolding experiment, but I re-experience the same
error. First of all, I use pdb2gmx for an input PDB structure, choose
OPLS/AA force field and vacuum settings (no waters).
Then I amke a box, and start simulations.
What I want to do is to compare the starting unfolded
Hello, I am getting an unknown error message in the submission of the G03
file:
QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.
# HF/6-31G OPT FREQ ^M ^M ARGUSLAB-GENERAT
'
Last state=GCL
TCursr= 909 LCursr= 20
Error termination via Lnk1e in
No. It contains a charged Gandolinium ion in the middle of a buckyball.
On Fri, Feb 25, 2011 at 2:59 AM, TJ Mustard musta...@onid.orst.edu wrote:
On February 24, 2011 at 10:29 AM Sergio Manzetti
sergio.manze...@vestforsk.no wrote:
Hello, I am getting an unknown error message
Hello every1,
I have a question about interpretation of g_rdf.
I have generated a plot with g_rdf (with -com flag) of a nanoparticle in
water, and it shows an unstable graph (y-axis) the first picoseconds , and
then a smoothing of the curve towards the zero the more r-value on the
x-axis
Hello, I am wondering if anyone has had luck installing glproto for a
functional Mesa package on Ubuntu? Thing is I am trying to install
wxmacmolplt-7.4.2 to view QM/MM results, but get nowhere without a
functional Open GL emulator.
Thanks
Sergio
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Does anyone know of a free-of-charge viewer for QM/MM results from G03, for
Ubuntu? It should be able to show electron orbitals, polarizabilities, bond
strength etc.
Sergio
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Hi everyone,
Does anyone have a suggestion for a free program to view QM/MM results from
Gromacs?
Thanks
The HiJacker
a.ka. S
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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
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
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
Dear all, I downloaded GMX from Ubuntu, and it was the 4.0.71 version. Does
anyone know or have the possibility to update UBUNTU with the latest GMX?
Cheers
Sergio
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Not really, there were no errors with ./configure
so I downloaded the version through ubunto sudo -apt get install gromacs
but it was old version
On Fri, Dec 24, 2010 at 10:53 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 24/12/2010 6:45 PM, Sergio Manzetti wrote:
Hi thanks, but if I
Thanks Justin, here is it the copy-out:
ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is
...@vt.edu wrote:
Quoting Sergio Manzetti sergio.manze...@vestforsk.no:
Thanks Justin, here is it the copy-out:
ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for a BSD
Thanks again J, is that compulsory each time one installs something new?
On Fri, Dec 24, 2010 at 2:50 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Quoting Sergio Manzetti sergio.manze...@vestforsk.no:
Thanks J, I think I will install Ubuntu entirely first, because I just
tried
to install
Well here is the FFTW message at make install:
/usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h'
/usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission
denied
/usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f'
/usr/bin/install: cannot remove
Justin, THe FFTW messagte was AFTER sudo make install.
On Fri, Dec 24, 2010 at 2:53 PM, Sergio Manzetti
sergio.manze...@vestforsk.no wrote:
Well here is the FFTW message at make install:
/usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h'
/usr/bin/install: cannot remove
Thanks, but I will start from scratch.
On Fri, Dec 24, 2010 at 3:13 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Quoting Sergio Manzetti sergio.manze...@vestforsk.no:
Justin, THe FFTW messagte was AFTER sudo make install.
Then you're not an admin. You can always do the installations
Dear Users, I am unable to get pass the first step of ./configure . This
step works, but when typing make it says:
no targets specified and no makefile found.
Should it be like this, or is it compulsory to use cmake?
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Dear users,
I made the a topology, but when I grompp for EM I get this weird message:
Fatal error:
Syntax error - File forcefield.itp, line 12
Last line read:
'Buckingham 1 no 1.0 1.0'
Found a second defaults directive.
I attached the topology here with
Hi thanks, but if I use make it says make no Makefile found...
On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 23/12/2010 9:12 PM, Sergio Manzetti wrote:
Dear Users, I am unable to get pass the first step of ./configure . This
step works, but when typing
I am trying to grompp a molecule, but get the same error again:
Program grompp, VERSION 4.5.1
Source code file: topio.c, line: 654
Fatal error:
Syntax error - File bzp.itp, line 1
Last line read:
'[ moleculetype ]'
Invalid order for directive moleculetype
For more information and tips for
2932 1 1.80e+02 5.00e+00 1.80e+02
5.00e+00
On Wed, Dec 22, 2010 at 7:36 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Sergio Manzetti wrote:
I am trying to grompp a molecule, but get the same error again:
Program grompp, VERSION 4.5.1
Source code file
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