Hi,
I am trying to install GROMACS-4.0.5, but while making mpirun with the
option --enable-mpi it gives the following sets of errors:
../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to
`ah_find'
../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to
`lam_ksign
On Mon, Jun 29, 2009 at 12:54 PM, Manik Mayur wrote:
> Hi,
> I am trying to install GROMACS-4.0.5, but while making mpirun with the
> option --enable-mpi it gives the following sets of errors:
>
read "making mdrun"
../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to
> `ah_fi
Manik Mayur wrote:
Hi,
I am trying to install GROMACS-4.0.5, but while making mpirun with the
option --enable-mpi it gives the following sets of errors:
../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to
`ah_find'
../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined
On Jun 28, 2009, at 10:46 AM, sharada wrote:
Hi,
I waited for it to finish for almost 5 days nothing happened
except creation of those files. I had posted a similar mail some
time back. Is there no solution for this. Is it something to do
with speed of the system? I ran the program
On Mon, Jun 29, 2009 at 1:51 PM, Mark Abraham wrote:
> Manik Mayur wrote:
>
>> Hi,
>> I am trying to install GROMACS-4.0.5, but while making mpirun with the
>> option --enable-mpi it gives the following sets of errors:
>>
>> ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined reference to
>
hello,
I have downloaded the tar file from the github and extracted the contents.
However I am unable to understand the README file as it is in a language other
than english. Could you kindly provide the instructions how to go about using
it.
thanks for the help
sharada
-- Original Message --
F
Hi
I want to install dssp programm in my linux machine but I am not getting it
from the website http://swift.cmbi.ru.nl/gv/dssp/. The linux executable given
in the website does not seems to work.Can any one suggest any alternative site
for downloading the current version of dssp.
Subarna
I did not test it, but
ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip offers the
sources and what I see from the readme.txt, it doesn't seem difficult
to compile it yourself.
--
###
Volker Wirth
Center for Medical Physics and Technology
Biophysics Group
FAU
On Jun 29, 2009, at 11:58 AM, sharada wrote:
hello,
I have downloaded the tar file from the github and extracted the
contents. However I am unable to understand the README file as it is
in a language other than english. Could you kindly provide the
instructions how to go about using it.
Hi GROMACS user group!
Maybe this should be aimed at the developers' mailing list... Anyway, I've been
having some problems (blowing up) when I tried to simulate a molecule such that
one part is coupled to a thermal bath using SD, and another part is not coupled
to any bath. Effectively, the
Hello,
with pdb2gmx I want to choose the protonation state of a GLN interactively.
When I choose +1 protonation state, I get the following error: Residue 'QLN'
not found in residue topology database. But the program has itself suggested
the QLN as the name of this protonation state!!
Would be
Yamin, Peyman wrote:
Hello,
with pdb2gmx I want to choose the protonation state of a GLN interactively.
When I choose +1 protonation state, I get the following error: Residue 'QLN'
not found in residue topology database. But the program has itself suggested
the QLN as the name of this protonat
OH! And a (-1) Alanine I can never have since pdb2gmx has no option for that?
It's my C-Terminus in the end! :-|
Von: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] im Auftrag
von Justin A. Lemkul [jalem...@vt.edu]
Gesendet: Montag, 29. Ju
Yamin, Peyman wrote:
OH! And a (-1) Alanine I can never have since pdb2gmx has no option for that?
It's my C-Terminus in the end! :-|
If the C-terminus bears the charge, then simply choose COO- as your C-terminus.
If the sidechain is somehow deprotonated, then you have to come up with the
Hi All,
1. Artificial Shear Flow: I am trying to do translocation studies and wanted to
generate a shear flow without actual water atoms. I checked the mail list and
it was mentioned that there is no velocity profile but an option to accelerate
the atoms in a group. But I wanted to get the she
Hi Gustavo,
On Jun 24, 2009, at 20:48 , Gustavo Fioravanti wrote:
we are trying to run mdrun_mpi in a public cluster of our
university. However, we got the following error:
/etc/profile.d/limits.sh: line 1: ulimit: max locked memory: cannot
modify limit: Operation not permitted
There ar
Hi,
I have a 72-lipid DPPC (MARTINI) system that I ran for 400ns in GROMACS
3.3.3. I picked a snapshot from the middle (~100ns), so I know it should be
equilibrated and be able to run for several hundred nanoseconds. If I use
GROMACS 4.0.3 (or 4.0.5) and 1, 2, or 4 processors, everything is great.
You are right. With MARTINI you often need an rdd bigger than default.
1.4 is reasonable.
On Jun 29, 2009, at 19:33, Michael Lerner
wrote:
Hi,
I have a 72-lipid DPPC (MARTINI) system that I ran for 400ns in
GROMACS 3.3.3. I picked a snapshot from the middle (~100ns), so I
know it sho
Hi everybody,
I used "g_sas" command in Gromacs4.0.3 to calculate volume of a protein. I
read Gromacs4_manual and found information on internet to understand
method(algorithm) used in Gromacs to calculate volume of a protein (or a
system consisting of water and protein). But I can not find the sol
hello gromacs users,
I am working with a silica structure which is parallepiped in
structure, i.e the unit cell is
46.4207 37.7846 18.9596 angles =90, 90, 120
I have a structure file in .xyz and .pdb but the units are in
Angstroms and for gromacs I assume that I need to convert these uni
Jennifer Williams wrote:
hello gromacs users,
I am working with a silica structure which is parallepiped in structure,
i.e the unit cell is
46.4207 37.7846 18.9596 angles =90, 90, 120
I have a structure file in .xyz and .pdb but the units are in Angstroms
and for gromacs I assume that I
hi,gmx-users，
I want to calculate the interaction energy between two group.
So I modify the .mdp file as follows:
energygrps = Protein sol
and make tpr file:
grompp -f md.mdp -c out.gro -p topol.top -o rerun.tpr -n index.ndx
mdrun -rerun md.trr -s rerun.tpr -o rerun.trr -c rerun.gro -e rer
Hi,
I have to install gromacs on a 30 node cluster computer. I only have access to
a specific space on the cluster, and it didn't have fftw3 installed on it. I
have installed it, and set the CPPFLAGS and LDFLAGS environment variables as
per instructions. The include and lib directories exist, a
Graham Kettlewell wrote:
Hi,
I have to install gromacs on a 30 node cluster computer. I only have access to
a specific space on the cluster, and it didn't have fftw3 installed on it. I
have installed it, and set the CPPFLAGS and LDFLAGS environment variables as
per instructions. The include
Justin A. Lemkul wrote:
-sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include
-sh-3.2$ export LDFLAGS=-I/hpc/software/packages/chemistry/fftw/lib
You want this line to contain -L, not -I.
That may have been a bit unclear; the LDFLAGS line should use -L, your CPPFLAGS
l
Hi Justin,
Thanks for your quick reply. It turns out that the stuff I posted was
malformed, as you pointed out, but it was a desperate attempt after a number of
goes, and I got that one wrong. I tried again using:
-sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/chemistry/fftw/include
-sh-3.2$
Graham Kettlewell wrote:
Hi Justin,
Thanks for your quick reply. It turns out that the stuff I posted was
malformed, as you pointed out, but it was a desperate attempt after a number of
goes, and I got that one wrong. I tried again using:
-sh-3.2$ export CPPFLAGS=-I/hpc/software/packages/ch
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Justin A. Lemkul
Sent: Tuesday, 30 June 2009 1:57 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] Installation with non standard location of fftw3
Graham Kettlewell wrote:
> Hi
Graham Kettlewell wrote:
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Justin A. Lemkul
Sent: Tuesday, 30 June 2009 1:57 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] Installation with non standard location of fftw3
It seems that your are fine for the energies but the properties
mentioned will be wrong.
On Jun 30, 2009, at 4:48 AM, Jinyao Wang wrote:
hi,gmx-users，
I want to calculate the interaction energy between two group.
So I modify the .mdp file as follows:
energygrps = Protein sol
and make tpr
30 matches
Mail list logo
