Dear Gromacs users,
I minimized a protein structure 1IARcompleted_WT.pdb, getting, among
others, the files 1IARcompleted_WT_minimized.trr and
1IARcompleted_WT_minimized_potential_energy.xvg . Looking at the latter
file showed the last frame to be at 217 ps:
.
.
@title Gromacs
On 14/02/2012 7:59 PM, Ehud Schreiber wrote:
Dear Gromacs users,
I minimized a protein structure 1IARcompleted_WT.pdb, getting, among
others, the files 1IARcompleted_WT_minimized.trr and
1IARcompleted_WT_minimized_potential_energy.xvg . Looking at the
latter file showed the last frame to be
This also was solved by the some extra minimisation steps.
I've forced with another problem :D
During npt equilibration my system have slightly expanded so my desired
volume and density were perturbed.
I've noticed the below options in npt wich could help me
ref_p= 1 1
compressibility
Dear Mark (or anybody else interested),
The .trr file does include the final (t = 217) frame - first, trjconv
said:
Reading frame 3 time 217.000
and second this is verified by converting the whole trajectory to .gro:
trjconv -f 1IARcompleted_WT_minimized.trr -s
Dear:
My receptor is membrane proteins,the I get protein-ligand complex.I want to
do MD simulations in DPPC.Can I use the GROMOS96 53a6 force field modified in
order to include Berger’s parameters for lipids?The topology for the ligand was
created employing the server PRODRG 2.5 Beta.How to
xiaojiong wrote:
Dear:
My receptor is membrane proteins,the I get protein-ligand complex.I
want to do MD simulations in DPPC.Can I use the GROMOS96 53a6 force
field modified in order to
include Berger’s parameters for lipids?
Sure, but there are other choices, as well.
The topology
I assume that you energy minimisd the system, but still have atomic clashes?
One thing which helped me in a similar case, was a short simulation at
low temperature with a really small timestep (about 3-5 magnitudes
smaller than the normal timestep). With this the atoms which clashes
move away
Dear all,
I'm trying to run FEP calculation of the ligand in the protein in water.
Performing NVT-dynamics for Lennard-Johnes perturbation using soft core results
in the following error:
There is no domain decomposition for 20 nodes...
I've checked out the log-file and found this:
Initial
shahid nayeem wrote:
Thanks Justin. I will try again. But please refer to some protocol if
you know and one last question that before doing umbrella sampling
simulation how can one be sure that the pulling is good and one should
go ahead with selecting window and doing umbrella sampling. In
Justin A. Lemkul wrote:
shahid nayeem wrote:
Thanks Justin. I will try again. But please refer to some protocol if
you know and one last question that before doing umbrella sampling
simulation how can one be sure that the pulling is good and one should
go ahead with selecting window and
Dear Alexey Zeifman,
From my experience it is just the nodes have to break down into some sort of
even multiple by dividing the domain decomposition size or vise versi. I
think somone elses answere was just to try it with a couple sizes for the
decomposition, as multiples of the number of
Alexey Zeifman wrote:
Dear all,
I'm trying to run FEP calculation of the ligand in the protein in water.
Performing NVT-dynamics for Lennard-Johnes perturbation using soft core
results in the following error:
There is no domain decomposition for 20 nodes...
I've checked out the log-file
On 15/02/2012 1:44 AM, lloyd riggs wrote:
Dear Alexey Zeifman,
From my experience it is just the nodes have to break down into some sort of
even multiple by dividing the domain decomposition size or vise versi. I think
somone elses answere was just to try it with a couple sizes for the
Hello,
I have done COM pulling simulation to pull a small molecule
(5-Fluorouracil) through a path. I want to see the rotational freedom for
the pulled over molecule during the SMD simulation. Is it meaningful to
calculate the rotational autocorrelation for a molecule which observes
external
On 14/02/2012 11:39 PM, Ehud Schreiber wrote:
Dear Mark (or anybody else interested),
The .trr file does include the final (t = 217) frame - first, trjconv
said:
Reading frame 3 time 217.000
and second this is verified by converting the whole trajectory to .gro:
trjconv -f
On 14/02/2012 11:01 PM, James Starlight wrote:
This also was solved by the some extra minimisation steps.
I've forced with another problem :D
During npt equilibration my system have slightly expanded so my
desired volume and density were perturbed.
I've noticed the below options in npt
Hi all,
Anybody can help me out! Thanks in advance?
In my test simulation, there are one Na^+ and one Cl^- (the distance of
1nm) in vacuum in a very big simulation box (10*10*10 nm^3). I calculated
the energies under two different conditions, coulombtype=PME vs
coulombtype=cut-off.
1.
Dear all,
I would like to calculate the PMF along a curved reaction pathway
using umbrella sampling. I just wonder if it is appropriate to use
g_wham to extract the PMF along the curved pathway? Any help would be
appreciated.
Hao Jiang
--
gmx-users mailing listgmx-users@gromacs.org
Hi all,
I know there has been a *lot* of discussion on the mailing list on
using freezegrps and potential pitfalls, but after having read much of
this discussion the past couple of days and the manual I still find
myself with questions and problems I'm hoping someone can help with.
What I want
Hi Gmxers,
Happy Valentine's Day!
Sorry, I am still simulating a protein that has water channel.
I was just wondering if there is a way to calculate the water density in the
channel throughout my trajectory.
I was lucky enough to run a NPT simulation. So I guess I can use g_energy to
directly
You can look at gromacs tool g_flux and g_count at:
https://github.com/orbeckst/g_count
Jianguo
From: Yao Yao ya...@ymail.com
To: gmx-users@gromacs.org gmx-users@gromacs.org
Sent: Wednesday, 15 February 2012, 10:38
Subject: [gmx-users] water channel
Hi
Dear Gmx Developer or Users,
Can anyone explain which section is for the parameters of improper
dihedral angle
on the file of ffbonded.itp ?
On the file of ffbonded.itp, there is not any comment to differentiate the
proper and improper
dihedral angle.
E.g. on thie file of ffbonded.itp in the
Tom wrote:
Dear Gmx Developer or Users,
Can anyone explain which section is for the parameters of improper
dihedral angle
on the file of ffbonded.itp ?
On the file of ffbonded.itp, there is not any comment to differentiate
the proper and improper
dihedral angle.
E.g. on thie file
Hi Gmxers,
Is there a way to calculate the density of water in a protein hydration layer,
like from 5 A to 10 A (radius) from the protein surface?
Thanks,
Yao--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Dear all,
I got confused about the usage of pull-geometry and pull-dim (pull-vector)
settings in the umbrella sampling simulations (not the pull / SMD
simulations).
In an umbrella sampling potential, U(r)=0.5*(r-r0)*(r-r0), are r and r0
referring to (A) the distance between the pulled group and
Mark,
due to hight density the volume of my system have been slightly increased
and during NPT phase I've obtained error
Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.
I'm using 0.9 for
Hi.
I've downloaded the charmm36 (gromacs-charmm36.ff_4.5.4.tgz) and
added some residues to it by editing the lipids.rtp file. I also plan
to use pdb2gmx to convert CHARMM-generated PDB files to GRO format.
The Gromacs manual suggests one should create a residuetypes.dat file
in the parent
Dear Gromacs users,
I am planing to use buckingham potential
for the non-bonded interactions of my system. I know that by changing the
nbfunc to 2 in [ defaults ] directive of topology will allow to use the
Buckingham potential , But I don't know how to specify
On 15/02/2012 4:45 PM, James Starlight wrote:
Mark,
due to hight density the volume of my system have been slightly
increased and during NPT phase I've obtained error
Fatal error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has
On 15/02/2012 5:42 PM, ramesh cheerla wrote:
Dear Gromacs users,
I am planing to use buckingham
potential for the non-bonded interactions of my system. I know that
by changing the nbfunc to 2 in [ defaults ] directive of topology will
allow to use the
On 15/02/2012 5:00 PM, Jernej Zidar wrote:
Hi.
I've downloaded the charmm36 (gromacs-charmm36.ff_4.5.4.tgz) and
added some residues to it by editing the lipids.rtp file. I also plan
to use pdb2gmx to convert CHARMM-generated PDB files to GRO format.
The Gromacs manual suggests one should
On 15/02/2012 5:09 AM, J. Nathan Scott wrote:
Hi all,
I know there has been a *lot* of discussion on the mailing list on
using freezegrps and potential pitfalls, but after having read much of
this discussion the past couple of days and the manual I still find
myself with questions and problems
Dear all
I am caculating delta G by umbrella sampling with position pull in
gromacs 4.5.after doing all of the steps when I want to use g_wham:
g_wham -it tpr_files.dat -if pullf_files.dat -o -hist
I have this error:
found pull geometry position and more than 1 pull dimension(3)
and it wants pdo
On 15/02/2012 2:46 AM, Qiao Baofu wrote:
Hi all,
Anybody can help me out! Thanks in advance?
In my test simulation, there are one Na^+ and one Cl^- (the distance
of 1nm) in vacuum in a very big simulation box (10*10*10 nm^3). I
calculated the energies under two different conditions,
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