On 2/17/2007 12:01 PM, Hu Zhongqiao wrote:
Arneh,
How does one build a topology using a different force field (say for
instance, oplsaa)? Is there a simple way to do it,
I think OpenEye (or someone else, I forget whom) has some sort of
automatic parameterization tool for OPLS that
Arneh,
> How does one build a topology using a different force field (say for
> instance, oplsaa)? Is there a simple way to do it,
I think OpenEye (or someone else, I forget whom) has some sort of
automatic parameterization tool for OPLS that automatically generates
parameters. Of course, th
Hi Mitch, thanks.
I'd like to use the OPLSA ff, to compare with other simulations that
I've run. So I can use the PRODRG to build an initial, then look at the
OPLSA ff to modify it, as you've suggested. I was just wondering if
there was a quick and easy way to do it, but I guess not!
Thank
Hi William,
did you look at Gerrits homepage
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/qmmm.html
you can further check out qmmm.c qm_gaussian.c in src/mdlib
Best,
Lars
> I was wondering about the QM/MM implementation in GROMACS. I want to
> use the QM program ORCA by Dr. Ne
Michael,
2) i get the same results when using md+NH thermostate
with two thermostates, or langevin dynamics (sd), the
error bars are somewhat larger with sd though.
Well, that's fine -- but it doesn't mean that everything is OK. NH has
known problems. There is also a bugzilla relating to this
Dear all,
A couple of weeks ago i reported a problem I
encountered with free energy calculations. I've
figured out by now what the problem was (a mistake in
the input, as usual ;) ... however, while searching
for the solution i made a couple of observations
that might be interesting for others (
I was wondering about the QM/MM implementation in
GROMACS. I want to use the QM program ORCA by Dr. Neese, but there is
little documentation about how GROMACS interfaces with the selected
(supported) QM program(s). I read somewhere there was an API for this
but have not found any more info. I
Arneh,
How does one build a topology using a different force field (say for
instance, oplsaa)? Is there a simple way to do it,
I think OpenEye (or someone else, I forget whom) has some sort of
automatic parameterization tool for OPLS that automatically generates
parameters. Of course, this is
If you wanted to study a collision, why do it at constant temperature?
Like David said, maybe you should equilibrate the droplet at 300K, add
a center of mass velocity to the droplet, and then study the collision
at constant energy. The real collision probably doesn't take place at
constant temper
My apologies. Magically things did work now :)
nick
On Fri, 2007-02-16 at 16:07 +0100, David van der Spoel wrote:
> Nicolas Bock wrote:
> > I named it conf.gro since genconf seemed to like that name. Where in the
> > gromacs manual does it describe the format of a gromos96 file? I only
> > fo
Nicolas Bock wrote:
I named it conf.gro since genconf seemed to like that name. Where in the
gromacs manual does it describe the format of a gromos96 file? I only
found references to the gromos96 manual but I couldn't find a file
format description in the online version of it either. Could you
Hi Nicolas,
It's on the website...
http://www.gromacs.org/documentation/reference/online/g96.html
Tsjerk
On 2/16/07, Nicolas Bock <[EMAIL PROTECTED]> wrote:
I named it conf.gro since genconf seemed to like that name. Where in the
gromacs manual does it describe the format of a gromos96 file
Nicolas Bock wrote:
I named it conf.gro since genconf seemed to like that name. Where in the
gromacs manual does it describe the format of a gromos96 file? I only
found references to the gromos96 manual but I couldn't find a file
format description in the online version of it either. Could you
I named it conf.gro since genconf seemed to like that name. Where in the
gromacs manual does it describe the format of a gromos96 file? I only
found references to the gromos96 manual but I couldn't find a file
format description in the online version of it either. Could you point
me to the right pl
Janne Hirvi wrote:
Hello!
I am trying to generate center of mass velocity to a water droplet so that I
could study the effect of impact velocity in the collision with a solid
surface.
First, I simply tried to generate extra velocity and compensate the increase in
temperature by decreasing other
Sunny wrote:
Dear Gmx developers,
The gmx/tutor examples include some mdp options not documented in the
Gromacs 3.3 user manual, such as those in the following list. Are they
deprecated or new parameters? Can I find a full list of mdp options?
bd-temp
nstcheckpoint
domain-decomposition
gb_al
Dear Gmx developers,
The gmx/tutor examples include some mdp options not documented in the
Gromacs 3.3 user manual, such as those in the following list. Are they
deprecated or new parameters? Can I find a full list of mdp options?
bd-temp
nstcheckpoint
domain-decomposition
gb_algorithm
nstgbr
Hello!
I am trying to generate center of mass velocity to a water droplet so that I
could study the effect of impact velocity in the collision with a solid
surface.
First, I simply tried to generate extra velocity and compensate the increase in
temperature by decreasing other velocity components.
Nicolas Bock wrote:
Hello list,
I need your help. I started playing around and began to set up my
crystal. I am having some issues though. I don't know whether that's
because something is wrong with my installation or with my inputs. Here
is what I did: I generated an xyz file with a 2 atom N
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