Or you can just use the git version.
--
Szilárd
On Wed, May 30, 2012 at 5:51 PM, Stephen Cox wrote:
> Hi Justin and Mark,
>
> Thanks once again for getting back.
>
> I've found the problem - it's actually a known bug already:
>
> http://redmine.gromacs.org/issues/901
>
> The dispersion correctio
Hi Gromacs Friends,
I am doing Justin-Umbrella sampling tutorial...
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html
After pulling I found the Chain A is moving away from protofibril but
reaches up to the other end of the cell..
So Is these
On 6/1/12 7:25 AM, rama david wrote:
Hi Gromacs Friends,
I am doing Justin-Umbrella sampling tutorial...
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html
After pulling I found the Chain A is moving away from protofibril but reaches
up to
Hi gromacs users,
I concatenated 7 trajectory files (each one has 10ns simulation) using
"trajcat". Then, when I used "gmxcheck", I get following error.
Reading frame 0 time0.000
# Atoms 68393
Precision 0.001 (nm)
Reading frame 13000 time 26000.000
*WARNING: Incomplete frame: nr 137
On 6/1/12 8:02 AM, Turgay Cakmak wrote:
Hi gromacs users,
I concatenated 7 trajectory files (each one has 10ns simulation) using
"trajcat". Then, when I used "gmxcheck", I get following error.
Reading frame 0 time0.000
# Atoms 68393
Precision 0.001 (nm)
Reading frame 13000 time 260
Hi Justin,
Thank you for your quick reply. I tried to concatanete the trajectory files
4 times. Three out of four try, I got same error massage.
But it worked for the last one.. It is a weird situation.. What could cause
this?
Turgay
2012/6/1 Justin A. Lemkul
>
>
> On 6/1/12 8:02 AM, Turgay Ca
On 6/1/12 8:54 AM, Turgay Cakmak wrote:
Hi Justin,
Thank you for your quick reply. I tried to concatanete the trajectory files 4
times. Three out of four try, I got same error massage.
But it worked for the last one.. It is a weird situation.. What could cause
this?
Sounds to me like your fi
Dear Gromacs users,
I have do simulation of surfactant at oil/water interface for a long time.
But I find it too difficult to get a reasonable interfacial tension. The
key question is the pcoupltype.
My system:
Box size: 3.0 * 3.0 * 13
> Molecule Number: decane 230, water 2041
> pcoupltype = se
Hello
If I have a force constant 287 kcal/(mol * A^2), the A stands for Angstrom and
I want to calculate this to kJ/(mol * nm^2), is it correct that I have to
multiply 4.19/0.01 = 419 to the force constant?
Is ithis true: 287 kcal/(mol * A^2) = 120253 kJ/(mol * nm^2)
Could this be a physica
One comment:
If the channel is horizontal orientated, and the COM of MOL lies in the
middle, you have two directions to go out of the channel: two the left
side (quasi negative distance) and to the right side (quasi positive
distance).
What happens with 'pull_geometry=distance' is, that only th
Hi,
First: Let me thank each and every one of you who took the trouble to fill out
our user survey. The resulting information is invaluable to us, and Mark Berger
of NVIDIA has been a tremendous help in assembling the results and statistics
for us. This WILL affect future development, and we ar
Hello,
I have found the excellent documentation for creating polymer
chains in GROMACS. I want to create several chains and pack
them into a volume, adjusting torsion angles to minimize
interactions with other chains (and self-interaction within a chain).
One method for doing this is the conf
There's a fair amount of interest for more general support for Monte
Carlo methods in GROMACS 5.0. However, there is no any current
support for configuration bias Monte Carlo (or any other kind of MC)
currently in the code.
On Fri, Jun 1, 2012 at 12:10 PM, Benjamin Haley wrote:
> Hello,
>
> I
Hi
>Monte Carlo methods in GROMACS 5.0.
Thats cool, when will GROMACS 5.0 be released?
Greetings
Lara
- Ursprüngliche Message -
Von: Michael Shirts
An: Discussion list for GROMACS users
CC:
Gesendet: 18:24 Freitag, 1.Juni 2012
Betreff: Re: [gmx-users] Configurational bias Mo
On 6/1/12 12:28 PM, Lara Bunte wrote:
Hi
Monte Carlo methods in GROMACS 5.0.
Thats cool, when will GROMACS 5.0 be released?
There is no release date yet. Version 4.6 is still coming together.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scien
On Fri, 2012-06-01 at 18:09 +0200, Erik Lindahl wrote:
> Hi,
>
> First: Let me thank each and every one of you who took the trouble to fill
> out our user survey. The resulting information is invaluable to us, and Mark
> Berger of NVIDIA has been a tremendous help in assembling the results and
Dear Hugh:
I can't answer your question, but I can address the error message that you see.
Basically, your semi-isotropic pressure coupling allows the surface area of the
water-decane
interface to get smaller as z increases and x and y decrease. In a system with
only water
and decane, this w
Your conversion is correct (Although you should use 1 cal=4.184 J (not 4.19)),
and yes, this is an absurdly strong force constant. I'm not sure what you mean
by
a physically realisitic value though.
-- original message --
If I have a force constant 287 kcal/(mol * A^2), the A stands for Angstro
I would like to thank for your generous gift Mark (NVIDIA) and for all GROMACS
team for the effort you made in developing the software and allowing us to use
it for free and on top of that for your great support in solving our problem on
this forum.
As Florian mentioned, the time it takes to
Dear Chris:
Thank you for your help. Maybe I can try it as this. First set x and y
fixed by setting compressibility = 0 4.5e-0.5 until the system
reaching equilibrium and then release. If it sounds reasonable. I am
trying to do it.
Dear Hugh:
I can't answer your question, but I can address the e
No, the point is that the equilibrium surface area is near zero in the context
of PBC and you need
special tricks to keep the system away from that equilibrium.
There will always be a force toward reducing the surface area of the
hydrophobic/hydrophilic interface. It is possible to disallow thi
Very thank you for your suggestion and being so kind. I will write a new
detailed subject and explain my purpose.
On Sat, Jun 2, 2012 at 10:23 AM, Christopher Neale <
chris.ne...@mail.utoronto.ca> wrote:
> No, the point is that the equilibrium surface area is near zero in the
> context of PBC a
Dear Gromacs users,
I am doing a membrane simulation. The system are two layers composed
by surfactants. other molecule are decane and water. The system like
this:
decane
---
surfactant
> ---
water
> ---
surfactant
---
decane
My research is t
On 2/06/2012 1:11 PM, Klniu wrote:
Dear Gromacs users,
I am doing a membrane simulation. The system are two layers composed by
surfactants. other molecule are decane and water. The system like this:
decane
---
surfactant
---
water
Sorry for my carelessness. Before nose-hoover, Parrinello-Rahman, I have
done v-rescale, berendsen already. tau_t = 0.1, tau_p = 0.5.
Hugh.
On Sat, Jun 2, 2012 at 12:43 PM, Mark Abraham wrote:
> On 2/06/2012 1:11 PM, Klniu wrote:
>
> Dear Gromacs users,
>
> I am doing a membrane simulation. The
25 matches
Mail list logo
