Mark Abraham wrote:
Dallas B. Warren wrote:
FYI, MediaWiki is the one used by Wikipedia (plus the one that use /
know). There are others.
In terms of integration with a Joomla site, I don't think there is
anything very good that works with MediaWiki. Was one floating around
awhile ago, a comp
Dallas B. Warren wrote:
FYI, MediaWiki is the one used by Wikipedia (plus the one that use /
know). There are others.
In terms of integration with a Joomla site, I don't think there is
anything very good that works with MediaWiki. Was one floating around
awhile ago, a component, but it didn't
Hi,
That what I did, I just hoped to be more lazy then I am already.
Itamar
- Original Message -
From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users"
Sent: Thursday, May 03, 2007 2:31 PM
Subject: Re: [gmx-users] rotational fit in XY plane only
Well,
Tsjerk Wassenaar wrote:
Hi Andrea,
On 5/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
Andrea Robben Browning wrote:
> I am trying to cut out a portion of a large equilbrated crystal to make
> a smaller crystal. I have been using the genbox command but since it
> tries to fill up a brick of spa
Hi Andrea,
On 5/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
Andrea Robben Browning wrote:
> I am trying to cut out a portion of a large equilbrated crystal to make
> a smaller crystal. I have been using the genbox command but since it
> tries to fill up a brick of space and my crystal is tric
Well, you can ofcourse run trjconv twice...
Tsjerk
On 5/3/07, Itamar Kass <[EMAIL PROTECTED]> wrote:
Dear Berk,
Thanks you very much for your quick and helpfully replay. If I may be a
bit nudnik and ask to get it as "rotxy+transxyz" instated of
"rotxy+transxy" thats will be wonderfully.
Thank
FYI, MediaWiki is the one used by Wikipedia (plus the one that use /
know). There are others.
In terms of integration with a Joomla site, I don't think there is
anything very good that works with MediaWiki. Was one floating around
awhile ago, a component, but it didn't do a very good job (wiki i
Dear Berk,
Thanks you very much for your quick and helpfully replay. If I may be a
bit nudnik and ask to get it as "rotxy+transxyz" instated of
"rotxy+transxy" thats will be wonderfully.
Thanks, Itamar
Best,
Itamar
Berk Hess wrote:
From: "Berk Hess" <[EMAIL PROTECTED]>
Reply-To: Discus
Andrea Robben Browning wrote:
I am trying to cut out a portion of a large equilbrated crystal to make
a smaller crystal. I have been using the genbox command but since it
tries to fill up a brick of space and my crystal is triclinic I end up
will dangling molecules. Is there any command that
I am trying to cut out a portion of a large equilbrated crystal to make
a smaller crystal. I have been using the genbox command but since it
tries to fill up a brick of space and my crystal is triclinic I end up
will dangling molecules. Is there any command that can cut a larger
configuration
The email list, manual, etc. are good source material...but I think there will
be added value in the wiki, even for answering specific questions. For
example, for questions about complex topics like free energy, integration
algorithms, parallel scaling, etc., it is rare that any single email me
Dear all
Does anybody, by any chance, have a Gromacs topology file for a
nitrosylated cysteine residue? If not, is anybody aware of information
for this residue in other program packages, or will PRODRG be my best
bet?
Thanks in advance
Daniel
--
Dr Daniel John Rigden Tel
Erik and all,
I think this is a great idea. I've been working on (and plans to work
more on) a bit of a free energy wiki/tutorial page beyond what's
already available; depending on how this develops I can
transfer/combine with what's already on the wiki.
As you probably know there are lots of th
2 maj 2007 kl. 15.13 skrev Berk Hess:
From: "Berk Hess" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] rotational fit in XY plane only
Date: Wed, 02 May 2007 14:10:59 +0200
From: Dr Itamar Kass <[EMAIL PROTECTED]>
Rep
Currently there is not.
I would like to have that feature as well.
can't you simply set all z-coordinates to zero and carry out a 3D fit as usual?
(you may get a problem with mirror images, but the handedness is anyway not
anymore uniquely defined once you project on 2D).
I don't think so. I
Hi Sona,
Also look at the energies. If Erik's local energy minimum is indeed an
all-time energy maximum (infinite energies, infinite forces), you're
starting structure is indeed your worry. But then again, if you
started from an energy minimized membrane, there's not much to
minimize anymore. Now
From: "Berk Hess" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] rotational fit in XY plane only
Date: Wed, 02 May 2007 14:10:59 +0200
From: Dr Itamar Kass <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
Berk Hess wrote:
>
>
>
>> From: Dr Itamar Kass <[EMAIL PROTECTED]>
>> Reply-To: Discussion list for GROMACS users
>> To: Discussion list for GROMACS users
>> Subject: [gmx-users] rotational fit in XY plane only
>> Date: Wed, 02 May 2007 19:44:12 +0800
>>
>> Hi all,
>>
>> I study a protein whic
From: Dr Itamar Kass <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: [gmx-users] rotational fit in XY plane only
Date: Wed, 02 May 2007 19:44:12 +0800
Hi all,
I study a protein which is moving toward an interface during my
simu
2 maj 2007 kl. 13.41 skrev Sona Aramyan:
Hi everybody
I'm trying to do em with l-bfgs integrator but it
finishes with 0 steps.
My system is 128dppc and 30 per lipid water.
when I'm using steep integrator it converged to
machine precision say 15 steps.
What I'm suggesting is that my system has
Hi everybody
I'm trying to do em with l-bfgs integrator but it
finishes with 0 steps.
My system is 128dppc and 30 per lipid water.
when I'm using steep integrator it converged to
machine precision say 15 steps.
What I'm suggesting is that my system has very bad
starting configuration and maybe it
Hi all,
I study a protein which is moving toward an interface during my
simulation. In order to analyse the why the protein is bound to the
interface I want to fit all my results. There is no problem with
translational fit, but I want to do rotational fit only in the XY plane.
Is there a nice way
Hi,
On May 2, 2007, at 10:01 AM, David van der Spoel wrote:
In all these things the format is less of an issue than the
content. The current website runs on Joomla and selected registered
users can edit parts of it.
Just read Erik's answer (that happens when you run away in the
middle
Dear Dallas and Mark
Thank you both for your replies.
George
-Original Message-
From: [EMAIL PROTECTED] on behalf of Mark Abraham
Sent: Wed 5/2/2007 1:42 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Electrostatic potential
Georgios Patargias wrote:
> Hi
>
> I
Hi,
Did you watch out for the wrong-hydrogen-in-DNA-termini-error when
using pdb2gmx with amberXX? I can't see that this would cause NaN-
energies, but it may be worth looking into.
/Erik
2 maj 2007 kl. 11.06 skrev Joern Lenz:
dear gromacs users,
i have the following problem:
i performe
dear gromacs users,
i have the following problem:
i performed an md simulation of a complex of protein and DNA (not covalently
linked) in a box of amber03_tip4p waters and the amber03 forcefield.
evereything is fine and i used the gromacs toools to extract a certain frame
out of the trajectory
From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Wall feature
Date: Tue, 01 May 2007 21:48:50 +0200
Luis Moux wrote:
Hi
There is a new feature in the CVS version of GROMACS that lets on
From: "merc mertens" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_energy sum
Date: Mon, 30 Apr 2007 10:00:11 +0200
hello,
you are right but "summing" over 1 term was done only for testing purposes.
first i
Dallas B. Warren wrote:
It's a good idea, but I don't think it will help a great
deal. The main
problem with frequently-occurring questions is that the
askers haven't
read the manual, the man pages, the web page, the FAQ or searched the
mailing list archives. In context, a Wiki would just be
Dear All,
There will be a workshop on problems of molecular docking and
applications of sophisticated optimization algorithms held as a
satellite conference of the European Conference on Complex Systems in
October 2007 in Dresden.
The molecular docking problem is to find the best orientation of t
Hi Dallas/Mark,
Actually, we can give it a try - I'll see if I have time to set
something up this week(end) and then assign all of you guys as
editors/admins too :-)
A wiki is most probably better than a forum, too. The main reason we
passed on the forum idea was that many users would onl
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