I want to simulate nanoparticles and I want to know if it is possible to
simulate nanoparticles by Gromacs or not? and if yes how can I simulate a
nanoparticle.
thanks
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On 5/01/2011 6:14 PM, Thomas Koller wrote:
Hello,
I have some questions concerning the implementation in Gromacs:
1) I want to model a rigid anion of an IL (fixed bonds and angles). The cation
is flexible. How can I do that without using constraint types? With LINCS or
SHAKE, I can only fix,
On 5/01/2011 7:26 PM, leila separdar wrote:
I want to simulate nanoparticles and I want to know if it is possible
to simulate nanoparticles by Gromacs or not? and if yes how can I
simulate a nanoparticle.
It's simple to say that it can be done, but it is not a kind of
simulation that GROMACS
Dear users,
I receive the following error when I entered the command "xpm2ps -f ss.xpm
-o ss.eps -di in.m2p"
Fatal error:
Library file in.m2p not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
I am using the Gromacs 4.05 on t
On 5/01/2011 7:37 PM, ahmet yıldırım wrote:
Dear users,
I receive the following error when I entered the command "xpm2ps -f
ss.xpm -o ss.eps -di in.m2p"
Fatal error:
Library file in.m2p not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB
Dear Sir,
Thanks for your prompt answer. In LIE method, if I will not
use the PME for coulombtype, then what is suitable for it? In gromacs
manual, there are several options under coulomb type.Which one I will select
for coulombtype and Vdwtype in .mdp file?
Your's sincerely
Devawati
Dear Mark,
I am using the Gromacs on the Ubuntu for month but have not encountered any
problems.I did a search in the file system of Ubuntu. I do not have a GMXLIB
folder in a file system.
What should I do?
05 Ocak 2011 10:42 tarihinde Mark Abraham yazdı:
> On 5/01/2011 7:37 PM, ahmet yıldırım
Mark, thanks for your reply.
The only problem are the improper dihedrals. I show you a example:
[ dihedraltypes ]
;improper ftypephik(phi) mult
...
A B C D 4 180 5.293 2
Sorry, I use ftype 4, not 2 :)
The impropers are listed in the dihedraltypes. The sequence is
ahmet yıldırım wrote:
Dear Mark,
I am using the Gromacs on the Ubuntu for month but have not encountered
any problems.I did a search in the file system of Ubuntu. I do not have
a GMXLIB folder in a file system.
What should I do?
If you're telling xpm2ps to use in.m2p, that file has to e
Hi,
We're in the process of transferring the domain name to a more convenient
registrar, and this will also require us to change DNS servers. Thus, you might
experience short interruptions in name resolutions for *.gromacs.org next week!
Cheers,
Erik--
gmx-users mailing listgmx-users@groma
Dear Justin and Mark,
Problem solved.Thanks for your helps
I copied to the directory /usr/share/gromacs/top it (in.m2p).
r...@ubuntu:/home/ab/Desktop# cp in.m2p /usr/share/gromacs/top
05 Ocak 2011 13:45 tarihinde Justin A. Lemkul yazdı:
>
>
> ahmet yıldırım wrote:
>
>> Dear Mark,
>>
>> I am us
Hello everybody,
Wish you a happy new year 2011.
I need to simulate a peptide in HFIP ( hexafluoro-propanol) solvent. As I was
browsing I came across a reprint in J.Phys.Chem.B 2001 titled
'Model of 1,1,1,3,3,3-Hexafluoro-propan-2-ol for Molecular Dynamics
Simulations' published from Gro
sharada wrote:
Hello everybody,
Wish you a happy new year 2011.
I need to simulate a peptide in HFIP ( hexafluoro-propanol) solvent. As
I was browsing I came across a reprint in J.Phys.Chem.B 2001 titled
*/'Model of 1,1,1,3,3,3-Hexafluoro-propan-2-ol for Molecular Dynamics
Simulations'/*
Hi folks,
Does anyone have timings/benchmarks for GMX running on Intel processors
codename Lynnfield, like Xeon X34??, Core i7 8?? or yet Core i5 7?? .
I am looking for both 1-node multi(4)-thread runs as well as multi-node
MPI runs. In particular, I am wondering how the cheaper but slower DMI
c
Dear GROMACS users,
We're trying to perform a MD simulation of a system with a hematin
group but realized that GROMACS does not have parameters for the ion
FE2+. We tried to include the parametrs in the file ions.itp but did not
suceed yet. Does anybody knows the right procedure to intr
Tanos Franca wrote:
Dear GROMACS users,
We're trying to perform a MD simulation of a system with a hematin
group but realized that GROMACS does not have parameters for the ion
FE2+. We tried to include the parametrs in the file ions.itp but did not
suceed yet. Does anybody knows the
Greetings friends!
I have a question this morning about the g_msd utility related to the output
generated by different flags.
I'm working with an LJ Liquid and am trying to determine the diffusion constant
for the system. I'm employing both the Einstein formulation and the Green Kubo
formula.
Dear all
I have generated a PMF curve for introducing a guest molecule into a
host molecule using the umbrella sampling method. The curve seems fine,
but there are no overlaps between histograms in the barrier region. To
circumvent this I have added more windows in this region and to ensure
sampli
On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote:
Dear all
I have generated a PMF curve for introducing a guest molecule into a
host molecule using the umbrella sampling method. The curve seems
fine,
but there are no overlaps between histograms in the barrier region. To
circumvent this I hav
Dear All,
I am planning to perform a simulation of a protein ternary complex with 2
ligands and Zn molecule. The protein has 2 chains with 430aa.Is it possible
to do simulation for the protein complex. I have got sufficient hardware
configuration for the dynamics study. As am new to perform such c
kala wrote:
Dear All,
I am planning to perform a simulation of a protein ternary complex with
2 ligands and Zn molecule. The protein has 2 chains with 430aa.Is it
possible to do simulation for the protein complex. I have got sufficient
hardware configuration for the dynamics study. As am ne
Hi Xavier
Many thanks for the reply. When I compare the two curves
Curve 1) lack of overlap in barrier region; force constant = 1000
Curve 2) with increased number of sampling windows with increased force
constant (note I have only increased the force constant of the windows
in the barrier region)
On Jan 5, 2011, at 5:01 PM, Gavin Melaugh wrote:
Hi Xavier
Many thanks for the reply. When I compare the two curves
Curve 1) lack of overlap in barrier region; force constant = 1000
Curve 2) with increased number of sampling windows with increased
force
constant (note I have only increased
Hi Xavier
Many thanks. Two more quick questions (both refering to barrier region):
Does the value of the force constant affect the height of the barrier
providing that there is reasonable overlap? Obviously there is a
compromise between the size of the constant and the number of windows.
If I incr
On Jan 5, 2011, at 6:03 PM, Gavin Melaugh wrote:
Hi Xavier
Many thanks. Two more quick questions (both refering to barrier
region):
Does the value of the force constant affect the height of the barrier
providing that there is reasonable overlap?
No! The force constant used does not affect t
On Tue, Jan 4, 2011 at 7:38 PM, Mark Abraham wrote:
> On 5/01/2011 5:53 AM, Elton Carvalho wrote:
>> [...] Does the larger timestep allowed by eliminating
>> high-frequency O-H vibrations outweigh the time needed by SETTLE?
>
> Most definitely. Typical GROMACS simulations report up to a few percen
On 2011-01-05 21.44, Elton Carvalho wrote:
On Tue, Jan 4, 2011 at 7:38 PM, Mark Abraham wrote:
On 5/01/2011 5:53 AM, Elton Carvalho wrote:
[...] Does the larger timestep allowed by eliminating
high-frequency O-H vibrations outweigh the time needed by SETTLE?
Most definitely. Typical GROMACS
Hi All,
I am a new user of Gromacs and Linux. I am using Ubuntu 10.10 and installed
Gromacs 4.5.3 following the instructions.
When I ran the demo, I found that when I pressed , the xterm window
which is supposed to appear separately just flashed and disappeared
immediately.
For instance, "the outpu
On 5/01/2011 8:38 PM, ahmet yıldırım wrote:
Dear Mark,
I am using the Gromacs on the Ubuntu for month buthave not encountered
any problems.
That's not the question I asked. If you're not using GMXRC properly, or
doing its work yourself by hand, you will run into problems eventually.
I did
Mao Mao wrote:
Hi All,
I am a new user of Gromacs and Linux. I am using Ubuntu 10.10 and
installed Gromacs 4.5.3 following the instructions.
When I ran the demo, I found that when I pressed , the xterm
window which is supposed to appear separately just flashed and
disappeared immediately.
On 5/01/2011 9:09 PM, Thomas Koller wrote:
Mark, thanks for your reply.
The only problem are the improper dihedrals. I show you a example:
[ dihedraltypes ]
;improper ftypephik(phi) mult
...
A B C D 4 180 5.293 2
Sorry, I use ftype 4, not 2 :)
The impropers are
Dear Email Sender,
Thank you very much for contacting me! Unfortunately, I am not available in the
office at the moment and cannot respond to your email. I will be able to handle
your request starting again Monday, January 10, 2011.
For all questions about CloudBroker, please contact the compan
On 5/01/2011 7:55 PM, devawati dutta wrote:
Dear Sir,
Thanks for your prompt answer. In LIE method, if I will
not use the PME for coulombtype, then what is suitable for it? In
gromacs manual, there are several options under coulomb type.Which one
I will select for coulombtype and
Hi Tsjerk,
Thanks for your more clarification, but when I am running the command
editconf -f pr.gro -o new_box.gro -density 1.04364e+03 (where pr.gro
is end.gro) the results I am getting are...
Read 12348 atoms
Volume: 97.5411 nm^3, corresponds to roughly 43800 electrons
Velocities found
syst
On 01/06/11, Navjeet Ahalawat wrote:
> Hi Tsjerk,
>
> Thanks for your more clarification, but when I am running the command
> editconf -f pr.gro -o new_box.gro -density 1.04364e+03 (where pr.gro
> is end.gro) the results I am getting are...
>
Please double check the contents of pr.gro are w
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