David,
> > I do not understand this.
> > Turning the restraints off is only affecting the highed of dG/dl
> and
> > turning it off means that you slowly go to zero.
>
> If you were computing a free energy of removing restraints,
> dG/dlambda
> should be negative, since it releases energy to tur
Hi all!
Well, first of all, sorry if it's on the wrong gromacs list, but from
what I could see on the website I could not find a clear indication on
where to put benchmarks.
Anyway, some time ago I asked the list for help on making this
benchmarks, on which I want to compare different com
We recently go into some acquisition of cheap SATA-based online storage.
It is still preferable to have online storage rather than DVD or tape.
And price-wise, it is cheap now to have TB-level storage.
Regards,
Yang Ye
Dallas B. Warren wrote:
Not exactly specific GROMACS question, but looking
karamyog singh wrote:
dear gromaxers.. how do i simulate a system under constant energy mode.
Don't perturb the energy that is, don't use temperature or pressure
regulation and use rigorous bond constraint algorithms. Be aware that
use of cut-offs is inherently non-conservative of energy.
Dallas B. Warren wrote:
Not exactly specific GROMACS question, but looking for some insight for
those who are sure to be encountering the same issues.
How are people now handling archiving the huge data files that are
produced when going to large simulation boxes for long periods of time?
Until
[EMAIL PROTECTED] wrote:
I am running a system of 185K atoms. The structure is energy minimized and the
dynamics run appears to be going smoothly until it just hangs. The job still
exists on the first node, but none of the 4 nodes are doing any work and I don't
get any error messages.
GROMPP:
We have modified an internal hard drive casing to convert the regular cable
into
a usb2 so that a cheap internal HD is functionally an external swappable drive.
A google search on "convert internal hard drive external" (without the quotes)
will bring you to some DIY sites. At regular intervals
Not exactly specific GROMACS question, but looking for some insight for
those who are sure to be encountering the same issues.
How are people now handling archiving the huge data files that are
produced when going to large simulation boxes for long periods of time?
Until recently it has been find
Jason O'Young wrote:
I have been having similar problems to this. I have posted to the
mailing list with the title "mdrun_mpi stops at random" but no one has
seen my reply :(.
it's been quite hectic on the list lately...
as always if you have a reproducible problem of a crash after a short
I have been having similar problems to this. I have posted to the
mailing list with the title "mdrun_mpi stops at random" but no one
has seen my reply :(.
It seems to be almost at random which of the processes falls...
Jason
I am running a system of 185K atoms. The structure is energy
min
[EMAIL PROTECTED] wrote:
Are you sure you want comm_mode = angular ? It seems like you have a
periodic system.
I do have PBC and a quick search indicates that angular is possible with PBC but
can lead to lincs errors or overlaps when using explicit solvent (although I
can't find any reasoning.
Hello everyone,
I'm simulating a nanotube on a substrate. My substrate is just a simple
impenetrable wall of closely packed atoms. To restrict the substrate to a
planar geometry I am using position restraints on substrate atoms as well as
using energy group exclusions (energygrp_exl = substrate sub
>Are you sure you want comm_mode = angular ? It seems like you have a
>periodic system.
I do have PBC and a quick search indicates that angular is possible with PBC but
can lead to lincs errors or overlaps when using explicit solvent (although I
can't find any reasoning. Anyone know of a referenc
[EMAIL PROTECTED] wrote:
I am running a system of 185K atoms. The structure is energy minimized and the
dynamics run appears to be going smoothly until it just hangs. The job still
exists on the first node, but none of the 4 nodes are doing any work and I don't
get any error messages.
The trajec
I am running a system of 185K atoms. The structure is energy minimized and the
dynamics run appears to be going smoothly until it just hangs. The job still
exists on the first node, but none of the 4 nodes are doing any work and I don't
get any error messages.
The trajectory looks good and no step
Lei Zhou wrote:
Hi,
Thank you for the answers. So I should use vacuum force field for the
all-atom NM analysis. But if I want to add a layer of explicit water
molecules as some papers did, which force field should I use?
Depends on how much water :)
Maybe read those papers a bit more carefu
Hi,
Thank you for the answers. So I should use vacuum force field for the
all-atom NM analysis. But if I want to add a layer of explicit water
molecules as some papers did, which force field should I use?
Thanks you.
Lei Zhou
On 5/16/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
Lei Zhou
Hi, I'm getting started with GMX and want to use AFM pulling, but I can't download the file pull.ppa from the website. How can I solve this problem? Thanks a lot. Ariel Alvarez
Yahoo! Autos. Más de 3.000 vehículos vendidos por mes.
¿Qué esperás para vender el tuyo?
Hacelo ahora y ganate
Message: 6
Date: Tue, 16 May 2006 23:02:15 +1000
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] 2 beginner?s questions
To: Discussion list for GROMACS users
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Sampo Karkola wrote:
> Hi,
>
>
Luther,
I actually thought I would switch off an atom`s charge and LJ interactions
if I transform it into a dummy atom. Is this wrong?
I am worried about the mass of the atom a heavy hydrogen is attached to.
In an amino group with heavy hydrogens the mass of the nitrogen is
decreased to about 8u
Lei Zhou wrote:
Hi,
Actually the major purpose was to extract the C-alpha components
from all-atom analysis, and then compare the result with other
approaches, like the PCA analysis or the GNM you mentioned. There was
some discussion on this before. I guess an easy way is still to use
g_nme
dear gromaxers.. how do i simulate a system under constant energy mode.
thanking you guys in advance.
-
karamyog.
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe reques
Hi,
Actually the major purpose was to extract the C-alpha components from all-atom analysis, and then compare the result with other approaches, like the PCA analysis or the GNM you mentioned. There was some discussion on this before. I guess an easy way is still to use g_nmens to generate an ense
[EMAIL PROTECTED] wrote:
Hi Lars,
I actually thought I would switch off an atom`s charge and LJ interactions
if I transform it into a dummy atom. Is this wrong?
I am worried about the mass of the atom a heavy hydrogen is attached to.
In an amino group with heavy hydrogens the mass of the nitroge
Hi Lars,
I actually thought I would switch off an atom`s charge and LJ interactions
if I transform it into a dummy atom. Is this wrong?
I am worried about the mass of the atom a heavy hydrogen is attached to.
In an amino group with heavy hydrogens the mass of the nitrogen is
decreased to about 8u
Oops, my bad.
Sampo
Check out these cool words by Mark Abraham:
Sampo Karkola wrote:
Hi,
also VMD is quite handy. You'll need pdb's for VMD, too.
Not true. VMD eats at least .gro, .g96, .trr and .xtc as well as .pdb
and a whole pile of others.
Mark
___
Sampo Karkola wrote:
Hi,
also VMD is quite handy. You'll need pdb's for VMD, too.
Not true. VMD eats at least .gro, .g96, .trr and .xtc as well as .pdb
and a whole pile of others.
Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www
You may also try SHIFTCALC : http://www.shef.ac.uk/NMR/mainframepage.html
Patrick
David van der Spoel a écrit :
Richa taimni wrote:
Dear all,
my question is that is it possible to calculate
chemical shift with the help of gromacs software.
You want to get the latest software from the David
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi,
I like a lot "chimera" (http://www.cgl.ucsf.edu/chimera/) It doesn't
currently support gromacs trajectories, but it does support trajectories
exported to single or multiple pdb files. It's incredibly easy to learn
and use. You can depict your mole
Richa taimni wrote:
Dear all,
my question is that is it possible to calculate
chemical shift with the help of gromacs software.
You want to get the latest software from the David Case group at Scripps
for that.
Regards,
Richa
__
Do You Yahoo!?
Hi,
also VMD is quite handy. You'll need pdb's for VMD, too.
Check out these cool words by Gale, Ella:
You can also use pymol. To use it you have to convert your trajectory to
a .pdb using trjconv, but pymol is quite easy to use.
> I am just starting my first dynamics and wonder if you could
Dear all,
my question is that is it possible to calculate
chemical shift with the help of gromacs software.
Regards,
Richa
__
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
+++ Hu Zhongqiao [Tue, May 16, 2006 at 04:06:42PM +0800]:
>
> I tried to input "Potential" but failed to get results.
>
Try again and hit the enter key twice. Works for me...
Maybe this should be added to the analysis FAQ?
--
Groeten,
Paul
___
g
Dear all,
I tried to use
g_energy to calculate potential energy in Gromacs 3.3. But I don't know how to
select after something was displayed as follows:
Select the
terms you want from the following
list-G96Bond
G96An
Title: RE: [gmx-users] 2 beginner´s questions
You can also use pymol. To use it you have to convert your trajectory to a .pdb using trjconv, but pymol is quite easy to use.
> I am just starting my first dynamics and wonder if you could help me with:
> 1. Want to use some graphical program t
Hi Luther,
why do you want to switch the charges of your heavy H's off? You could
just switch the charges and LJ interactions off, and leave the masses
as they are.
Best,
Lars
[EMAIL PROTECTED] wrote:
Dear Gromacs users,
I want to perform a thermodynamic integration using heavy H´s in my
Hi,
On May 15, 2006, at 10:02 PM, Lei Zhou wrote:
Hi,
I am trying to convert the binary Hessian matrix (nm.mtx) into a
readable ascii format. According to the recommendations on this
email list, I rename the nm.mtx to nm.trr and tried to use gmxdump.
However, there is an error message li
From: Tomoshi Kameda <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: [gmx-users] kappa in Generalized reaction field
Date: Tue, 16 May 2006 14:35:31 +0900
> >
> >Do we want to keep this code at all?
>
> Good question.
> I think simulating io
38 matches
Mail list logo
