Hello
I want to simulate a protein in water and observe its behavior alone and then
in the presence of ligand. I have read somewhere that NPT MD is best for
pro-lig complexes as it resembles the in vitro and in vivo conditions
(conformational changes,biomolecular reactions, binding etc.). So My
Hi Dr. Bowerman:
Thanks for replying.
Happy holidays!
Best,
Wei-Hsiang
--
Wei-Hsiang Weng (翁偉翔)
Department of Life Sciences
Tzu-Chi University
No.701, Sec. 3, Zhongyang Rd. Hualien 97004, Taiwan
Tel.: +886-975-232-245
2016-01-26 11:18 GMT+08:00 Samuel Bowerman :
> Hello Wei-Hsiang,
>
> G_c
Hello Wei-Hsiang,
G_correlation will print a 0-1 value automatically. If you provide the
"-mi" flag, then the output is raw mutual information (range 0 to
infinity). You can not "set a range" for the values; they are what they
naturally are. You simply choose what formalism to work in (correla
Dear all:
I'm using the generalized correlation analysis tool developed by Lange and
Grubmüller. Does anyone know the option for setting the range of
correlation values? Say, 0 to 1?
Any advice would be appreciated, thanks in advance.
Best,
Wei-Hsiang
--
Wei-Hsiang Weng (翁偉翔)
Department of Life
Hi Albert,
I have to concur with Mark's point, it's not hard at all to pick (or
happen to benchmark) circumstances under which one code is
significantly faster than the other.
In order to understand the differences, please share:
- GROMACS logs
[ - full hardware & software specs, compilers, CUDA,
Hello all,
Has anyone parameterized Brefeldin A or GDP for Amber force fields? I wish
to simulate a protein with BFA and GDP as ligands, but have so far been
unable to find parameters for these molecules.
I have a procedure to do so using RED and Gamess, but understand this is a
difficult process
On 1/25/16 4:33 PM, abdus sabuj wrote:
Hi Justin,
I have used these following commands in npt and final .tpr production.
grompp -f npt.mdp -p topol.top -c nvt.gro -o npt.tpr
grompp -f final.mdp -p topol.top -c npt.gro -o final.tpr
...which explains everything. You're not preserving the
Hi Justin,
I have used these following commands in npt and final .tpr production.
grompp -f npt.mdp -p topol.top -c nvt.gro -o npt.tpr
grompp -f final.mdp -p topol.top -c npt.gro -o final.tpr
Thanks,
Sabuj
On Mon, Jan 25, 2016 at 1:55 PM, Justin Lemkul wrote:
>
>
> On 1/25/16 2:41 PM, abdu
Hi,
It's not clear what you intend to do to preserve neutrality, but you can
get charges to change incrementally over time with the slow-growth
free-energy perturbation code. Whether that's a useful model remains to be
seen...
Mark
On Mon, Jan 25, 2016 at 9:06 PM AshutoshAkshay Shah
wrote:
> H
Hello GROMACS users,
I am simulating a graphene based supercapacitor. I want to change the
charge of each particle at the electrode surface such that the voltage of
the electrochemical cell remains constant. I know the formula to be used
for this, but I have no idea how to implement it. I want to
On 1/25/16 2:41 PM, abdus sabuj wrote:
Hi Justin,
Here is the mdp file I used for NPT equilibration...
integrator = md
nsteps = 1000
dt = 0.001
nstenergy= 1000
nstxout = 1000
nstvout
On 1/25/16 2:50 PM, Chang Woon Jang wrote:
Dear Mark,
Thank you for the information. I have changed the topol.top file now like
I put another three lined for posres right below each itp, DGA.itp and
J230.itp.
; Include forcefield parameters
;#include "forcefield.itp"
; Include chain top
Dear Mark,
Thank you for the information. I have changed the topol.top file now like
I put another three lined for posres right below each itp, DGA.itp and
J230.itp.
; Include forcefield parameters
;#include "forcefield.itp"
; Include chain topologies
#include "DGA.itp"
#ifdef POSRES
#includ
Hi Justin,
Here is the mdp file I used for NPT equilibration...
integrator = md
nsteps = 1000
dt = 0.001
nstenergy= 1000
nstxout = 1000
nstvout = 1000
vdw-type
Dear Sabuj,
It would be difficult to help without more info (size of system, contents of system, .mdp file, etc...). I have not used simulated annealing in years, and when I used the software in the past, it was mostly structure determination from unknown phases (cooling an unknown partial st
Hi Nicolas, have you installed the latest binutils before going through the
installation? I used gcc/5.3.0, but the versions you've tried should work
fine, too.
Koji
On Mon, Jan 25, 2016 at 12:56 PM, Nicolas Cheron <
nicolas.cheron.bou...@gmail.com> wrote:
> Hi,
>
> All my installations are made
On 1/25/16 1:51 PM, abdus sabuj wrote:
Hi Mark,
I have equilibrated my system very well before the production run at 300K,
but at time zero, the temperature is at 321K.
Here is the fluctuations I am getting.
time (ns) temperature (K)
0 321
2 315
4
Hi Mark,
I have equilibrated my system very well before the production run at 300K,
but at time zero, the temperature is at 321K.
Here is the fluctuations I am getting.
time (ns) temperature (K)
0 321
2 315
4 333
6 358
Hi,
What fluctuations were you seeing over the time segments?
Mark
On Mon, 25 Jan 2016 19:25 abdus sabuj wrote:
> Dear gmx users,
>
> I am trying to get viscosity as a function of temperature. So I have put
> the following annealing inputs to the mdp file.
>
> ;simulated anneling
> annealing
Hi,
See
http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx
Mark
On Mon, 25 Jan 2016 19:19 Chang Woon Jang wrote:
> Dear Gromacs Users,
>
> I have two types of molecules. The topology file was separated by one
> (topol.top) and two (DGA.itp, and J230.itp).
>
> The form
Hi,
That could be evidence of a bug. If you can upload your grompp inputs, tpr
and log files to a new issue on redmine.gromacs.org we can consider further.
Cheers,
Mark
On Mon, 25 Jan 2016 15:27 Andreas Mecklenfeld <
a.mecklenf...@tu-braunschweig.de> wrote:
> Dear all,
>
> I want to perform an
Dear gmx users,
I am trying to get viscosity as a function of temperature. So I have put
the following annealing inputs to the mdp file.
;simulated anneling
annealing = single
annealing-npoints = 6
annealing-time= 0 2000 4000 6000 8000 1
annealing-temp= 300 310 320 330 340 350
Dear Gromacs Users,
I have two types of molecules. The topology file was separated by one
(topol.top) and two (DGA.itp, and J230.itp).
The format I made in topol.top is
#include "DGA.itp"
#include "J230.itp"
[ system ]
; Name
DGA and J230
[ molecules ]
; Compound#mols
Other_chain_A
Hi,
Thanks. Indications are that you also need an updated binaries package.
Specifically, there's a test that the compiler accepts the avx2 flag, which
is passing. But some other part of the infrastructure isn't working
(probably the linker) because the next test fails.
Mark
On Mon, 25 Jan 2016
Hi,
All my installations are made from a clean build directory. I am
using CentOS release 6.6 and the CPU is Intel Xeon CPU E5-2650 v3 @
2.30GHz. Here is the exact list of command that I have used (as I said, I
have also tried with gcc4.9.3 and gcc5.2):
module purge
module load gcc/4.8.5
cd /home
Hi,
Neither of the two papers you mentioned use the Berger lipid parameters, rather
they both use purely GROMOS lipid force fields. This is plain GROMOS 45A3 for
the Chandrasekhar et al. paper (using older, original, GROMOS DPPC lipid
charges). This force field doesn't reproduce the properties
Dear all,
I want to perform an alchemical change of state of a molecule in TIP3P,
where I do only change the partial charges of the atomtypes. To control
my results, I perform two MD runs with the different charge sets
respectively.
I'm interested in the Coulomb-14 interactions of the solute
Hi all,
I would appreciate your opinion on a quite often discussed topic.
I am doing simulations of triglycerides and phosphoglycerides, and I am
currently using the combination of gromos96 53a6 and Berger Lipid parameters as
suggested in Justin Lemkuls Tutorial.
If I am right, this combination
I think you can figure this out after playing 5 min with the make_ndx tool,
but here it goes:
"r ILE | r LEU | r VAL" will select all the isoleucines, leucines and
valines in your system.
Cheers,
On 25 January 2016 at 12:23, Shima ebrahimi wrote:
>
>
> Dear Users,
>
> I want to determine hydr
Dear Users,
I want to determine hydrophobic interaction between ligand and protein
using g_mindist. However, how can I identify non-polar atoms and specify
them in the index file.Could anyone help me?
Regards,
Shima
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