Dear users,
What I see the difference between the .gro file given at the examples in the
tutor directory and my own .gro file is that
the last lines gives 0.000 0.000 0. in my file and in the examples it is
not.
I assume it is the dimension of the box, isn' it?
I built up the gro file u
On Tue, 4 Dec 2007 05:56:22 +
pragya chohan <[EMAIL PROTECTED]> wrote:
Dear users
I was tyring to run an npt simulation of membrane. My mdp is:
The changes you observe are not dramatic. Why this seems a problem
to you?
I could not find the actual values of cut-off for vdw interactions.
X
Dear Gromacs users,
Thanks for the messages.
Tsjerk,
I was not aware that capital letters denote unpolite. I just used them to
highlight the problem so others can easily pick out. Thanks for the suggestions
as well.
I modified the file:
***
Dear users
I was tyring to run an npt simulation of membrane. My mdp is:
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5 ; total 100 ps.
nstcomm = 1
nstxout = 250
nstenergy = 100
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = PME
vdwtype = cut-off
; Berendsen temper
Quoting jahanshah ashkani <[EMAIL PROTECTED]>:
> Hi,
> I have got a segmentation fault error when I run mdrun for 1ns. I would be
> glad if you let me know what is going on and how can I solve it.
> Thank you very much.
What happened before the segmentation fault?
-Justin
>
> Best,
>
>
> Jahans
What is the system?
What steps did you perform before this?
What was the command line?
What is the actual error output?
A lot more information is required before anyone will be able to even
have a guess at what is going on.
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biolog
Hi,
I have got a segmentation fault error when I run mdrun for 1ns. I would be glad
if you let me know what is going on and how can I solve it.
Thank you very much.
Best,
Jahanshah Ashkani,
PhD student of Biotechnology & Genetics,
University of the Western Cape,
Biotechnology Department,
Priva
As noted by someone, please post the last couple of lines of the .gro
file you provide to grompp.
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61
Quoting JMandumpal <[EMAIL PROTECTED]>:
>
> Dear Justin,
>
> I made some changes in my .mdp file, but the result is same.
>
> My box size, as mentioned in the previous mail, is 20.1 A. The cut off I used
> is 8 angstrom.
>
> I attach the input file here.
> **
>
Dear Justin,
I made some changes in my .mdp file, but the result is same.
My box size, as mentioned in the previous mail, is 20.1 A. The cut off I used
is 8 angstrom.
I attach the input file here.
**
cpp= /lib/cpp
define = -DPOSRES-DF
Quoting huan <[EMAIL PROTECTED]>:
> i found that the molecules are not at the center of
> the box everytimes after the simulation..they always
> appear at a side of the box..izzit it is related with
> the energy minimization?
> thankz
http://wiki.gromacs.org/index.php/Periodic_Boundary_Condi
i found that the molecules are not at the center of
the box everytimes after the simulation..they always
appear at a side of the box..izzit it is related with
the energy minimization?
thankz
Be a better pe
Hi,
This does not look right indeed. You should give more details about your
simulations parameters: Pcoupling, T, compressibility, [chol], bix size,
time step ...
XAvier
Hi, all:
I'm trying to embed cholesterol molecules into a DOPC bilayer in a coarse
grained model.
The force field and coor
Hi,
I installed a serial version of GMX, and am trying to install an mpi
version. I did a make distclean, and followed standard procedures, and
am getting the following errors during make mdrun:
Any suggestions ? Thank you !
##
(cd ./sr
No, the membrane is between the two "2" numerals.
With 3-4 ns equilibration, the total potential difference between the
two sides of the membrane should be zero, and the potential should be
continuous at the box edges. So there is some other problem
On Dec 3, 2007 7:39 PM, Pedro Alexandre de Araú
Hi, all:
I'm trying to embed cholesterol molecules into a DOPC bilayer in a coarse
grained model.
The force field and coordinates for a pure DOPC bilayer and for cholesterol
were obtained on the MARTINI's site. I randomly replace a DOPC molecule with
a cholesterol molecule and do the energy minimiz
If I understood your graph correctly, the "valleys" represent the
contribution from the headgroups and the central "peak" lies in the middle
of the bilayer.
It can be seen that the two monolayers are not equivalent which is probably
due to lack of equilibration.
You can convince yourself by measur
Hi,
I calculated the electrostatic potential using g_potential across a
large 416-lipid POPC bilayer from a 200 ps trajectory. The bilayer is
well-hydrated, and has zero charge.
However, I get a very odd potential which starts off at 0.0 and ends
at 0.6 V, but is not monotonically increasing all
Hi,
I got these grid cells when I used pressure coupling. Check ur box size
fluctation. when i got there, my box was exploding, however the
calculation didnt crash. check the trajactory to see if there is big box
size changes.
Belquis
> Dechang Li wrote:
>> Dear all,
>>
>> During my simula
Dear Gromacs users,
I am using Gromacs on a system for which I have modified LJ
interactions which i have to treat using fully tabulated potentials.
-Electrostatics are handled using PME.
-I have User for vdwtype in my mdp options, several energy groups and
matching table_X_Y.xvg files for the
Hi Robert,
without looking any further into the data (no impropers on the
phosphates seem to be OK though): Are you sure you need a protonated
phosphate?
Regards
Christian
Robert Fenwick schrieb:
>
> Here are the topology file lines that I have added to my version of
> ffG43a1.rtp
>
> It shou
From: Steven Kirk <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Coarse-graining and tabulated non-bonded
potentials- will write
Date: Mon, 03 Dec 2007 16:17:03 +0100
Berk Hess kindly answered my original query below. I ha
Berk Hess kindly answered my original query below. I have some more
questions that might be of general interest to the list, so I'm
conducting another step of the conversation in the list.
-
Date: Mon, 26 Nov 2007 14:18:36 +0100
From: "Berk Hess" <[EMAIL PROTECTED]>
Subject: RE: [gmx-users]
Here are the topology file lines that I have added to my version of
ffG43a1.rtp
It should just work if you add these lines to this file. If anyone
has any comments then I would be happy to have them, this is the
first time I have done this.
Bryn
[ GTP ]
[ atoms ]
GN9NR-0.
wangcl wrote:
Dear all users,
I want to analyze Hydrogen-bond among water molecules using "g_hbond"
command. We use periodic boundary conditions in the simulation box.
The question is: I don't know whether this "g_hbond" tool considers the
"periodic boundary conditions", that is,
whe
Dear all users,
I want to analyze Hydrogen-bond among water molecules using "g_hbond"
command. We use periodic boundary conditions in the simulation box.
The question is: I don't know whether this "g_hbond" tool considers the
"periodic boundary conditions", that is,
whether this tool c
From: Brian Helfrich <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Writing initial coordinates to trajectory files
Date: Fri, 30 Nov 2007 12:55:20 -0500
Berk Hess wrote:
The initial coordin
Jestin,
Please don't use all capitals. As Mark has pointed out several times, that's
considered shouting. You're probably frustrated that things don't work
according to your expectations, but the frustration comes from you not
knowing what your doing. Don't blame us for that, go read a manual.
If
Li Qiang wrote:
Dear all users,
I want to plot the velocities of center of mass for my peptide. Reading
from 3.3 manual, there seems to be two ways--g_com and g_traj.
However,
1, g_com can not be found in /usr/local/gromacs/bin. Is there anything
missed for my installation?
2, $> g_traj -f m
Dear all users,
I want to plot the velocities of center of mass for my peptide. Reading
from 3.3 manual, there seems to be two ways--g_com and g_traj.
However,
1, g_com can not be found in /usr/local/gromacs/bin. Is there anything
missed for my installation?
2, $> g_traj -f md.trr -s md.tpr -o
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