- Original Message -
From: shahab shariati
Date: Sunday, May 30, 2010 16:28
Subject: [gmx-users] separation of two strands of DNA during of simulation
To: gmx-users@gromacs.org
> Dear Justin
>
> thanks for your attention.
>
> You said that separation of two strands of DNA during of si
Dear Qian:
Debiasing equations for this can be found by analogy to eq. 16 and 17
in the the original Torrie and Valleau US paper: "Nonphysical sampling
distributions in Monte Carlo free-energy estimation: Umbrella sampling".
Alternatively, I used a simple method in
doi:10.1016/j.cplett.20
While Mark's answer is entirely complete, I'll just add one more idea
in case you don't know where to put the OG.
1. Go into your .gro file and change the SER to an ALA
2. pdb2gmx to place the hydrogens around the CB
3. EM
4a. Copy the EM output .gro file into 3 directories, and in each one
o
Dear Francisco:
1. gromacs already has an spce.itp file. Try using that one directly
and see if your answer changes. If it does, then one file is in error.
2. the density of spc/e is not 1g/cc. First thing, you should try to
reproduce an RDF from the literature for which you use exactly the
Dear Emanuel:
We need you to be much more specific.
1. What link?
2. Even though it might be in the link, you should still provide us
with a general protocol that you followed.
Chris.
-- original message --
I am using Gromacs to calculate solvation of free energy calculation.
First I tri
Dear GMX Users,
I want to run Gromacs on a multiprocessor PC.
The MPI files are correctly installed and the gromacs is also configured.
However, at the end of configuration section, an Error appears that the FFTW
can not be found!
Indeed, the FFTW is already installed but the configuration can
nanogroup wrote:
Dear GMX Users,
I want to run Gromacs on a multiprocessor PC.
The MPI files are correctly installed and the gromacs is also configured.
However, at the end of configuration section, an Error appears that the
FFTW can not be found!
Indeed, the FFTW is already installed but
Hello all !!
I was playing around with template.c and stuck in a problem.
In the program inside the do loop i.e;
/* This is the main loop over frames */
do {
/* coordinates are available in the vector fr.x
* you can find this and all other structures in
* the types directory unde
On Sun, 2010-05-30 at 21:43 +0530, Chandan Choudhury wrote:
> Hello all !!
>
>
> I want to execute the statements under if loop after each 50 ps time.
I'd just forget any if clauses in the loop and run the program with -dt
50, which gives the same result.
--
--
- Original Message -
From: you zou
Date: Friday, May 28, 2010 14:41
Subject: [gmx-users] add missing atom
To: gmx-users@gromacs.org
> Hi everyone,
> I have one question about adding atoms that are missing in residue. This atom
> is OG in SER amino acid. I don't know how can I add this
Hi Chandan,
The problem is that with floating points the equality in
> if (fr.time == (4000.000 + (50.0 * inc)))
is very unlikely to be satisfied at any time. To compare floating
point numbers, you'll have to check whether the value is within a
certain interval. But Jussi's approach is far more
nanogroup wrote:
Dear Justin
Many thanks for your response
This is the exact phrase:
"
Use CPPFLAGS and LDFLAGS if the library is installed in a
non-standard location. (see FAQ at http://www.gromacs.org)
If you dont care about performance you can also specify 'fftpack'
to use a slower set o
Hi , I am having a problem in installing gromacs-4 in a suse linux in a
powerpc ibm machine. The problem is that
1. I first installed fftw in the following way :for single
precision./configure --enable-float --enable-threads
--prefix=/N/u/tg-jmondal/BigRed/UTIL/fftwmakemake install
Then for
- Original Message -
From: jagannath mondal
Date: Monday, May 31, 2010 5:44
Subject: [gmx-users] fftw library problem in gromacs installation
To: gmx-users@gromacs.org
Thanks for the detailed post.
| > Hi , I am having a problem in installing gromacs-4 in a suse linux in a
powerpc ibm
Hi,
I am having a problem in a cluster which is IBM PowerPC 970MPs and running
SUSE linux and it has IBM XL C & Fortran compliers ( xlf, xlc ).
I was trying to install gromacs 4 there using open-mpi which is already
installed using ibm compilers.
Here is my configure command:
./configure --p
- Original Message -
From: Sanku M
Date: Monday, May 31, 2010 13:00
Subject: [gmx-users] gromacs installation problem in ibm powerpc system
To: gmx-users@gromacs.org
> Hi,> I am having a problem in a cluster which is IBM PowerPC 970MPs and
> running SUSE linux and it has IBM XL C &
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