Dear Users,
actually, libXm.2.dylib is missing.
Could anyboby tell me how to get this file?
Thanks
>liang wrote:
>> Dear Users,
>>
>> i would like to install gromacs on Mac OSX tiger 10.4.10, and i download
>> this dmg file from ftp site.
>> after i installed successfully, i tried to test s
liang wrote:
> Dear Users,
>
> actually, libXm.2.dylib is missing.
You may want to install fink and the finkcommander, which provides you
with a graphical user interface for installing free software packages
(including gromacs...). Anyway, once you have that you need to install
openmotif.
>
>
liang wrote:
> Dear Users,
>
> actually, libXm.2.dylib is missing.
>
> Could anyboby tell me how to get this file?
This belongs to Motif or Lesstif libraries. Of all the gromacs tools,
only ngmx requires it, and since it's a very optional tool, you can turn
off building it with a configure opt
I want to perform simulation of transmembrane
peptide. I have a perseuillibrated POPO (hydrated)
bilayer (using CHARMM),containing more than 32,000
atom. But when I try to convert ".pdb" to ".gro" using
"pdb2gmx", it shows the following error
Fatal error:
Residue "popc" not found in resi
Moutusi Manna wrote:
I want to perform simulation of transmembrane
peptide. I have a perseuillibrated POPO (hydrated)
bilayer (using CHARMM),containing more than 32,000
atom. But when I try to convert ".pdb" to ".gro" using
"pdb2gmx", it shows the following error
The role of pdb2gmx is
I want to perform simulation of
trans-membrane
peptide. I have a equilibrated POPC (hydrated)
bilayer (using CHARMM),containing more than 32,000
atom. But when I try to convert ".pdb" to ".gro" using
"pdb2gmx", it shows the following error
Fatal error:
Residue "popc" not found in residue
Moutusi Manna wrote:
I want to perform simulation of
trans-membrane
peptide. I have a equilibrated POPC (hydrated)
bilayer (using CHARMM),containing more than 32,000
atom. But when I try to convert ".pdb" to ".gro" using
"pdb2gmx", it shows the following error
Fatal error:
Residue "pop
Dear GMX-users:
I've searched the list but couldnt find something usful for me, and this is
how I did it so far :
source /opt/intel/fce/version/bin/ifortvars.sh
export F77=ifort
export CPPFLAGS=-I/home/xin/programs/fftw312/include
export LDFLAGS=-L/home/dong/programs/fftw312/lib
configure --prefi
You get plenty of "these are the same file" error look:
/people/mail/mariag/gromacs-3.3.1/man/man1/anadock.1' are the same file
try to make install to a different folder than the one you extracted the
source (.tgz)
PWD = /people/mail/mariag/
%tar xvfz gromacs-3.3.1.tgz
%cd /people/mail/mariag/gro
This works for me:
% vim /etc/ld.conf
/opt/intel/mkl/8.0/lib/em64t/ <<<= only if you have installed MKL
/opt/intel/fce/9.0/lib/
/opt/intel/cce/9.0/lib/
then run
% ldconfig
If you wish, you may also add the 32bit libs:
/opt/intel/mkl/8.0/lib/32/ <<<= only if you have installe
Hi,
Well, I have a much simpler solution - there is no reason whatsoever
to use fortran on ia32 or x86-64 since Gromacs will always use the
much faster SSE assembly loops.
Cheers,
Erik
On Sep 13, 2007, at 8:44 AM, Diego Enry wrote:
This works for me:
% vim /etc/ld.conf
/opt/intel/mkl
Hi.
Yes, but that is the "gcc solution". No prblem with those, except for giving
away the "challenge" to make it work with intel compilers.
Basically: I couldn't find a way much better. The way I trid in the time I
tried, included compilation of the loops and only the loops using gcc to
make the
Hello,
I am looking for a way in Gromacs that I could apply a uniform shear. I
have looked through the manual, and it seems that the methods for applying
shear are using the cos_acceleration option or the deform option. The deform
option may work for me. However, I was reading in Allen and
toma0052 wrote:
Hello,
I am looking for a way in Gromacs that I could apply a uniform shear. I
have looked through the manual, and it seems that the methods for applying
shear are using the cos_acceleration option or the deform option. The deform
option may work for me. However, I was rea
Hi,
I am wanting to solvate a protein w/o adding H2O to its interior.
Reasons:
1. I am interested to know how the structural H2Os behave initially
w/o interference from added H2O.
2. Added H2O also introduce steric constraints that prevent EM from
achieving its goal, even w/o constrain
Hello,
Thanks for the rapid response, although I am not sure I completely
understand what you mean. The accelerate option adds a constant acceleration
to whatever atoms I choose with acc_grps. However, if I want a uniform
shear, I need to give atoms an acceleration dependent on their positio
toma0052 wrote:
Hello,
Thanks for the rapid response, although I am not sure I completely
understand what you mean. The accelerate option adds a constant acceleration
to whatever atoms I choose with acc_grps. However, if I want a uniform
shear, I need to give atoms an acceleration dependen
Hello everybody,
I have a system made of lipid and water and I want to calculate the
components of the lipid-lipid, lipid-water and water solvent
interactions (LJ+electrostatics). I know there is already a lot of
explanations about that kind of stuff on the mailing-list. I have
carefully rea
Hi guys,
A stupid question: I got myself confused with this
shuffling/deshuffling thing, which I
shouldn't have been doing with protein in the first place. So this
are my steps, done
on the same 4 nodes, please tell me whether I was supposed to do any
deshuffling
of .trr and .gro files, and fol
Dear GMX users,
I uploaded a wrapper to run the Multiprot program using output from
Gromacs to the user contributions in the GMX site. Multiprot,
http://bioinfo3d.cs.tau.ac.il/MultiProt/ , performs structural alignment
based on geometry, not sequence, and thus it allows the alignment of two
protei
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