Nicolas Sapay wrote:
Hello everybody,
I'm trying to use a DPPC bilayers with charges from the Jacob Sonne et
al. study (Biophys J., 2007). The problem is that the authors have
defined a single group for the whole DPPC molecule. This allow them to
define new accurate charge for the head group
WU Yanbin wrote:
Hi, Everybody,
And I found that if this simulation is on gromacs3.3, the warning
becomes error.
Yours
Sincerely,
indeed, since this is not implemented. you canhowever use table
potentials that differe betw
Patricia Soto Becerra wrote:
Hi,
I have a question regarding the calculation of hydrogen bond lifetimes
in g_hbond:
Line 1094 of gmx_hbond.c v 1.16.2.11 2006/04/02 (which is equivalent to
line 1121 of gmx_hbond.c v 1.28 2006/08/30) reads:
t = hb->time[i] - hb->time[0] - 0.5*dt;
leading to
naga raju wrote:
Dear gmx users,
I have some problem regarding scalling factor of cluster. Here I have
given cluster specifications, installation procedure, i request you go
through query and suggest me.
Here is the system specifications:
Master node: Intel Pentium 4, 3.0 GHz with 64HT 800
Hi, Everybody,
And I found that if this simulation is on gromacs3.3, the warning becomes
error.
Yours
Sincerely,
WU Yanbin
Message: 7
Date: Wed, 13 Jun 2007 21:35:42 -0500
From: "WU Yanbin" <[EMAIL PROTECTED]>
Subject: [gmx-users]
Dear gmx users,
I have some problem regarding scalling factor of cluster. Here I have given
cluster specifications, installation procedure, i request you go through query
and suggest me.
Here is the system specifications:
Master node: Intel Pentium 4, 3.0 GHz with 64HT 800 MHz FSB/2
WU Yanbin wrote:
Hi,
When I use both LJ and Buckingham non-bonded interaction in my
topology file, specially like the following:
[ nonbond_params ]
; ij func c6 c12
OW OW 1 ...
; ij
Nicolas Sapay wrote:
Hello everybody,
I'm trying to use a DPPC bilayers with charges from the Jacob Sonne et
al. study (Biophys J., 2007). The problem is that the authors have
defined a single group for the whole DPPC molecule. This allow them to
define new accurate charge for the head group
Hi,
When I use both LJ and Buckingham non-bonded interaction in my topology
file, specially like the following:
[ nonbond_params ]
; ij func c6 c12
OW OW 1 ...
; ij func a
Hello everybody,
I'm trying to use a DPPC bilayers with charges from the Jacob Sonne et
al. study (Biophys J., 2007). The problem is that the authors have
defined a single group for the whole DPPC molecule. This allow them to
define new accurate charge for the head group atoms and the first at
Hi,
I have a question regarding the calculation of hydrogen bond lifetimes in
g_hbond:
Line 1094 of gmx_hbond.c v 1.16.2.11 2006/04/02 (which is equivalent to
line 1121 of gmx_hbond.c v 1.28 2006/08/30) reads:
t = hb->time[i] - hb->time[0] - 0.5*dt;
leading to the time series 1, 3, 5,.. th
Hello,
From the mailinglist archive It is said the scalar virial from the g_energy
vir=(1/3)*(vir(xx)+vir(yy)+vir(zz))=-0.5*sum(iinteractions are pairwised.
I tried to verify this by using the relation
PV=(2/3)*E(kin)+(1/3)*sum(iAll instantaneous virial, kinetic energy, pressure and volume can b
I could understand if it was doing this within pdb2gmx or something
that was constructing a topology file. I'm observing this behavior
when using editconf to simply convert files to another format or apply
box dimensions etc. Anyway, I submitted a bugzilla about it. This
isn't such a big problem -
On 6/14/2007 1:14 AM, Erik Lindahl wrote:
Hi Robert,
On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote:
These are all fine points. However, the question I'm asking is why do
Gromacs tools change atoms named OXT in PDB files to O2? Of course
there are always workarounds i.e. just simply change
I want to make hole in center of popc bilayer . how
?can i do it by make-hole program?(cx,cy=?)
You can read the manual.
Once you unpack the files you will have README.hole
That file contains installation instructions (gromacs-3.1.4 only) and a link to
usage instructions.
_
Robert Johnson wrote:
These are all fine points. However, the question I'm asking is why do
Gromacs tools change atoms named OXT in PDB files to O2? Of course
there are always workarounds i.e. just simply change the atom name in
the coordinate file. However, I was wondering if anyone knew why thi
Hi Robert,
On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote:
These are all fine points. However, the question I'm asking is why do
Gromacs tools change atoms named OXT in PDB files to O2? Of course
there are always workarounds i.e. just simply change the atom name in
the coordinate file. Howev
These are all fine points. However, the question I'm asking is why do
Gromacs tools change atoms named OXT in PDB files to O2? Of course
there are always workarounds i.e. just simply change the atom name in
the coordinate file. However, I was wondering if anyone knew why this
happened. I suppose I
Andrei Neamtu wrote:
Dear Mark,
Thank you for your reply!
I thought that maybe the accessibility were the problem. I don't figure
how to set the working directory of say node 1 to my current working
directory on node 0.
I setup node 1 to be able to access node 0 through ssh with no password
>It's hard to work out your problem, but it sounds like you haven't read
>manual section 3.2 yet. Please do so, and get back to us.
>
>Mark
Thanks Mark!
I will check manual. I am really sorry for bothering!
BEST REGARDS
___
gmx-users mailing list
Thanks a lot Mark and Ye, I will try both alternatives!
Andrei
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don'
Hi,
I think that the terminal oxygen atoms should not be named OXT for the
amber forcefields but rather OC1 and OC2. To check this look in the top
folder at the ffamberXX.rtp file.
Hope this helps
Tom
--On Tuesday, June 12, 2007 15:30 -0400 Robert Johnson
<[EMAIL PROTECTED]> wrote:
Hell
Setting up a NFS shall be handy.
On 6/13/2007 5:13 PM, Andrei Neamtu wrote:
Dear Mark,
Thank you for your reply!
I thought that maybe the accessibility were the problem. I don't
figure how to set the working directory of say node 1 to my current
working directory on node 0.
I setup node 1 to
Andrei Neamtu wrote:
Dear Mark,
Thank you for your reply!
I thought that maybe the accessibility were the problem. I don't figure
how to set the working directory of say node 1 to my current working
directory on node 0.
I setup node 1 to be able to access node 0 through ssh with no password
Dear Mark,
Thank you for your reply!
I thought that maybe the accessibility were the problem. I don't
figure how to set the working directory of say node 1 to my current
working directory on node 0.
I setup node 1 to be able to access node 0 through ssh with no
password but the problem rem
Dear all
I want to make hole in center of popc bilayer . how
can i do it by make-hole program?(cx,cy=?)
thanks
8:00? 8:25? 8:40? Find a flick in no time
with the Yahoo! Search movie showtime shortcut.
http://
linfu wrote:
> Dear GMX community!
>
> I have question about PBC and link cell based cutoff method.
>
> (1)
> for example one water molecule,if only H atom of one water molecule
> move out of box, however, O atom are still in the box. does this H atom
> will need to be image back to the box throu
Dear GMX community!
I have question about PBC and link cell based cutoff method.
(1)
for example one water molecule,if only H atom of one water molecule
move out of box, however, O atom are still in the box. does this H atom
will need to be image back to the box through PBC,or just ignore it
unt
Andrei Neamtu wrote:
Dear gmx users,
I have problems in running a simulation on several nodes using the
-multi option:
I make the .tpr files for different temperatures (I want to use the REMD
code)
grompp -f param0.mdp -po param0.out.mdp -c conf.gro -p topol.top -o
sim0.tpr
grompp -f par
Dear gmx users,
I have problems in running a simulation on several nodes using the
-multi option:
I make the .tpr files for different temperatures (I want to use the REMD code)
grompp -f param0.mdp -po param0.out.mdp -c conf.gro -p topol.top -o sim0.tpr
grompp -f param1.mdp -po param1.out.m
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