Hello all,
Now I want to have a simulation of water and methane system, but when I wrote a
methane.itp and the force field file, it could not run correctly. I used tip4p
water and the opls-aa methane. According to the simulation with NPT, not only
the pure methane system, but also the water and
Dear all,
Does that mean the atoms will shrink and adjust at the time inflategro step
and
this closely packed lipids will stay apart? Because as you said the energy
of course will be high on selected atoms during first EM step.
Could you suggest me that, can I proceed as such with my system, since
Dear GMX Users,
I am trying to execute Gromacs 4.6.1 on one of the GPU server:
*OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release)
*gcc*: 4.7.2
CUDA Library paths
#CUDA-5.0
export CUDA_HOME=/usr/local/cuda-5.0
export PATH=$CUDA_HOME/bin:$PATH
export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/li
Dear James:
As always, check the primary literature. The Amber99SB ff was introduced with
an 8A cutoff and PME: http://www.ncbi.nlm.nih.gov/pubmed/16981200
Other cutoffs are at your discretion. I am, for instance, using this ff with a
1.0 nm cutoff and PME because I am using it with the Stockho
I'm implementing a TOP file reader, and I have a question about an ambiguity in
the format. The [ pairs ] block lists atom pairs that should be handled
specially (exclusions and 1-4 interactions). In addition, the gen-pairs flag
can indicate that pairs are generated automatically. But all the
Hi! Recently I've been simulating a system comprised of water and LiCl ions
in different arrangements. Depending on the arrangements I get different
responses in terms of performances. The box is tetragonal (but I heard from
other people in my lab that they had a performance hit also in cubic boxes
Dear users,
I used the following commands to get diffusion constants (every 10 ns) of a
simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory
every 20 ps). I looked at RMSD vs average structure, RMSD vs starting
structure, Radius of gyration, RMSD matrix. This simulation has r
Hello All,
My simulation system is composed of DNA and want to pull both of the primes
at the same time towards each other.
I have tried every possible set of parameters in pull code...and i am not
able to pull them together.
it's like ...
the DNA molecule is aligned along Y-axis and if want to p
> Date: Wed, 27 Mar 2013 15:14:19 +0100
> From: Mark Abraham
> Subject: Re: [gmx-users] compilation of gromacs-4.5.4 with fftw-3.3
> for double precision versition
> To: Discussion list for GROMACS users
> Message-ID:
>
> Content-Type: text/plain; charset=UTF-8
>
> Yes, --en
Dear Justin,
Thank you very much for your suggetions.
BW
Fugui
At 2013-03-27 22:15:23,"Justin Lemkul" wrote:
>On Wed, Mar 27, 2013 at 10:11 AM, xiao wrote:
>
>> Dear Justin,
>> Thank you very much for your reply.
>> I found that the speed of implict MD is slower that explict MD. For
>> examplex
On Wed, Mar 27, 2013 at 10:11 AM, xiao wrote:
> Dear Justin,
> Thank you very much for your reply.
> I found that the speed of implict MD is slower that explict MD. For
> examplex, the speed of an explict MD for a protein of 300 amino acids is
> about 3ns per day, however, the implicit solvent is
Yes, --enable-long-double is useless for FFTW+GROMACS.
Mark
On Wed, Mar 27, 2013 at 3:03 PM, Qinghua Liao wrote:
> Hi all,
>
> Finally I compiled it successfully when I used the following commands:
>
> 1077 ./configure --prefix=/usr/users/iff_th2/liao/fftw-3.3
> --enable-threads --enable-shared
Dear Justin,
Thank you very much for your reply.
I found that the speed of implict MD is slower that explict MD. For examplex,
the speed of an explict MD for a protein of 300 amino acids is about 3ns per
day, however, the implicit solvent is about 1.5ns per day.
With respect to the accuracy of im
On Wed, Mar 27, 2013 at 9:57 AM, 라지브간디 wrote:
> Thanks for the mail justin.
>
>
> In charmm27.ff, the value for bonded are in b0 and ko format, whereas the
> gromos uses them in different way? If so, how do i convert between them?
>
>
Please consult the manual, Chapters 4 and 5 for all the releva
Hi all,
Finally I compiled it successfully when I used the following commands:
1077 ./configure --prefix=/usr/users/iff_th2/liao/fftw-3.3
--enable-threads --enable-shared --enable-mpi CC=gcc
1078 make
1079 make install
1080 history | grep export
1081 export CPPFLAGS=-I/usr/users/iff_th2/
Thanks for the mail justin.
In charmm27.ff, the value for bonded are in b0 and ko format, whereas the
gromos uses them in different way? If so, how do i convert between them?
The value i incorporated for specific atoms are from published journals. Thanks
in advance.
On 3/27/13 2:15 AM, �
On Wed, Mar 27, 2013 at 9:27 AM, xiao wrote:
> Dear Gromacs users:
> I did a protein MD using implicit solvent and Amber 99SB force filed.
> However, i found that the implicit solvent is not faster than explicit
> solvent, and what is worse is that it is also not accurate.
> The system is a prote
Dear Gromacs users:
I did a protein MD using implicit solvent and Amber 99SB force filed. However,
i found that the implicit solvent is not faster than explicit solvent, and what
is worse is that it is also not accurate.
The system is a protein-ligand complex. Firstly, i run a minimization, and t
cd
mkdir fftw3.3
cd Desktop
wget http://www.fftw.org/fftw-3.3.tar.gz
tar xzvf fftw-3.3.tar.gz
cd fftw-3.3
./configure --prefix=/home/manchu/fftw3.3 --enable-threads --enable-sse2
--enable-shared
make
make install
cd
mkdir gromacs_install
cd Desktop
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4
Dear Justin,
Thanks very much for your reply! Yeah, I did not add the option of
--enable-shared for compilation of gromacs 4.5.4, but it still failed after
I added this option for the compilation.
For the compilations I posted in the last e-mail, I do add the option of
--enable-shared in compilati
Hi,
Gromacs calls fsync for every checkpoint file written:
fsync() transfers ("flushes") all modified in-core data of (i.e., modi-
fied buffer cache pages for) the file referred to by the file descrip-
tor fd to the disk device (or other permanent storage device) so that
On 3/27/13 6:57 AM, Qinghua Liao wrote:
Dear gmx users,
I tried to compile gromacs 4.5.4 with double precision, but it failed. The
reason was a little wired.
Firstly, I used the following commands to compile gromacs 4.5.4 together
with fftw 3.3 for serial and parallel version with single prec
On 3/26/13 11:13 PM, Christopher Neale wrote:
Dear Matthew:
Thank you for noticing the file size. This is a very good lead.
I had not noticed that this was special. Indeed, here is the complete listing
for truncated/corrupt .cpt files:
-rw-r- 1 cneale cneale 1048576 Mar 26 18:53 md3.cpt
On 3/27/13 5:40 AM, Zalikha Ibrahim wrote:
Good day to all GMX users,
I have two trajectories, 0-10ns and 10-20ns. I merged both .trr file using
trjcat with option -overwrite.
trjcat -f npt.trr npt2.trr -o npt_cat.trr -overwrite
Converted into .xtc and then I tried using the g_cluster tool
On 3/27/13 2:15 AM, 라지브간디 wrote:
Hello gmx,
I have LJ parameter value of C (epsilon = 0.0262 kcal/mol, sigma = 3.83) O
(epsilon = 0.1591. sigma = 3.12) in charmm format and wants to use them in
gromos43a1 or charmm27 force field in gromacs.
Could you tell me how do i convert them to gro
Dear gmx users,
I tried to compile gromacs 4.5.4 with double precision, but it failed. The
reason was a little wired.
Firstly, I used the following commands to compile gromacs 4.5.4 together
with fftw 3.3 for serial and parallel version with single precision, and I
made it successfully.
1014
Good day to all GMX users,
I have two trajectories, 0-10ns and 10-20ns. I merged both .trr file using
trjcat with option -overwrite.
>trjcat -f npt.trr npt2.trr -o npt_cat.trr -overwrite
Converted into .xtc and then I tried using the g_cluster tool in order to
cluster the trajectories.
> g_clus
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