Hi Guys,
I met a problem when I ran QM/MM/MD using semi-empirical method in
gmx407+mopac7,
-
"Subscript out of range on file line 659, procedure moldat.
Attempt to access the 0-th element of variable eheat.
Aborted"
--
Hi Mark,
I can confirm that the fix works.
Setting -DGMX_ACCELERATION=Power6 sets to these
/* Define to a macro mangling the given C identifier (in lower and upper
case), which must not contain underscores, for linking with Fortran. */
#define F77_FUNC(name,NAME) name
/* As F77_FUNC, but
Hello, I've got a pdb file,but while I convert it to gro files, I met such
problem:
Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while
sorting atoms
I find that in the rtp files of the ff files, the H atom linked with C-alpha
is called H, but in the pdb file, the sa
On 13/09/2011 4:14 PM, aiswarya pawar wrote:
Mark,
the command line goes like this-
g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500
This command line is not using an index file. The index groups defined
for the grompp that produced the .tpr are being used (which may be the
default ones, dependi
dear Xian,
open the PDB using text editor and replace the name...
good luck
From: xiansh...@gmail.com
To: gmx-users@gromacs.org
Date: Tue, 13 Sep 2011 15:36:41 +0800
Subject: [gmx-users] how to handle different atom names between pdb and rtp
files.
Hello, I’ve got a pdb file,but wh
g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 if the index name not given it
takes the default index file, so there isnt any wrong in selecting the
atoms.
On Tue, Sep 13, 2011 at 1:24 PM, Mark Abraham wrote:
> On 13/09/2011 4:14 PM, aiswarya pawar wrote:
>
> Mark,
>
> the command line goes like th
Ok I tried that and it doesn't work:
There's a fundamental difference between chains/no-chains topology, namely
the existence of peptide bond between chains, and the different protonation
state on the termini.
In the chain-based topology there are several termini, and less peptide
bonds.
This caus
On 13/09/2011 6:11 PM, Shay Teaching wrote:
Ok I tried that and it doesn't work:
There's a fundamental difference between chains/no-chains topology,
namely the existence of peptide bond between chains, and the different
protonation state on the termini.
In the chain-based topology there are sev
Dear Gmx users
I have run MD on carbon nanotube with solvated drug molecules inside and
outside the tubes. Kindly would you please let me know how I
can visualize and calculate the amount of molecules only inside the carbon
nanotube during MD process. May I know what keywords I should use in graph
Message: 2
Date: Mon, 12 Sep 2011 18:38:57 +0300
From: ? ??
Subject: [gmx-users] g_lie (again..)
To: gmx-users@gromacs.org
Message-ID:
Content-Type: text/plain; charset="iso-8859-1"
Hi all,
Could anyone please refer to me to a paper or other resource that explains
in detail (specifi
can i get the amber94 topology file for so4 molecule?
--
Asha Jayachandran
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meisam valizadeh kiamahalleh wrote:
Dear Gmx users
I have run MD on carbon nanotube with solvated drug molecules inside and
outside the tubes. Kindly would you please let me know how I
can visualize and calculate the amount of molecules only inside the
carbon nanotube during MD process. May
Hi Yun,
Have you read http://ambermd.org/formats.html?
In particular, this note:
"""
NOTE: *the atom numbers in the following arrays that describe bonds, angles,
and dihedrals are coordinate array indexes for runtime speed. The true atom
number equals the absolute value of the number divided by
Unsubscribe me Please
--
Om Prakash Sharma
Ph.D Scholar & DIT JRF
Centre for Bioinformatics
Pondicherry University
Pondicherry-605014
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Dear Justin,
Thanks a lot for your reply.
Here I am providing the data and explaining the problem in detail:
I hope that it will help you in understanding in a better way.
Considering the tetramer as 'abcd'. 'ab' as one dimer and 'cd' as
another, I want to separate 'ab' and 'cd'. Length o
Shilpi Chaurasia wrote:
Dear Justin,
Thanks a lot for your reply.
Here I am providing the data and explaining the problem in detail:
I hope that it will help you in understanding in a better way.
Considering the tetramer as 'abcd'. 'ab' as one dimer and 'cd' as
another, I want to separate
Ok,
Using -DGMX_ACCELERATION=Power6 brings a plethora of new errors during
the compilation.
Firstly, including config.h inside the fortran .F kernel files for
power6 is causing problems with
their parsing using xlf. adding -WF,-qfpp didn't help. Had to provide a
modified xlf.cfg config file
On 14/09/2011 12:20 AM, Marcin Zielinski wrote:
Ok,
Using -DGMX_ACCELERATION=Power6 brings a plethora of new errors during
the compilation.
Firstly, including config.h inside the fortran .F kernel files for
power6 is causing problems with
their parsing using xlf. adding -WF,-qfpp didn't help
Thank you very much for your help, Justin.
I tried it with those mdp options:
title = INITIAL_EM0
cpp = /lib/cpp
constraints = all-bonds
integrator = md
rlist = 0.0
rcoulomb= 0.0
rvdw= 0.0
pbc
Matthias Ernst wrote:
Thank you very much for your help, Justin.
I tried it with those mdp options:
title = INITIAL_EM0
cpp = /lib/cpp
constraints = all-bonds
integrator = md
rlist = 0.0
rcoulomb= 0.0
rvdw
Hi Guys,
I met a problem when I ran QM/MM/MD using semi-empirical method in
gmx407+mopac7,
Subscript out of range on file line 1002, procedure domldt.
Attempt to access the 161-th element of variable labels.
Aborted
-
Has anyone met this before?
Thanks,
Dear experts,
I am working on a pure polymer melt system under NPT and at a given T,
pressure is increased up to around 1000 bar. However, the phase diagram of
the polymer is indicating that at this T, as pressure is increased to above
500 bar, system falls below the melting point.
I mean I am do
It certainly is, you just need to focus on a property that changes between the
phases and that is obtainable from the MDSs. For a transition from liquid to
solid, things like RDF, SDF, dihedral fractions and diffusion coefficients
might provide some insight.
You have the trajectories, why don'
Hey Zach,
You may be best off starting from the free energy code. It can be used to
perturb charges and other things during a simulation.
Hope it helps,
Tsjerk
On Sep 13, 2011 2:55 AM, "Zach Levine" wrote:
Hi everyone,
I'm trying to implement time-varying charges for various ions located
in
Hi
I am working with RHEL 6 beta, I unable to install the FFTW package while
installation I found the following error,
make[3]: Leaving directory `/home/Ithayaraja/Desktop/
fftw-3.3.1-beta1/tools'
make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/tools'
Making all in m4
make[
On 14/09/2011 3:24 PM, ITHAYARAJA wrote:
Hi
I am working with RHEL 6 beta, I unable to install the FFTW package
while installation I found the following error,
There is no error reported in what you have shown.
make[3]: Leaving directory `/home/Ithayaraja/Desktop/
fftw-3.3.1-beta1/tools'
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