gurgo> I want to perform MD Equilibration run under position restrained for
gurgo> 200ps. Bond
gurgo> distances were constrained using the LINCS (Linear Constraints)
algorithm,
gurgo> the water molecules were restrained using the SETTLE algorithm. In order
to
gurgo> do this I have modified nsteps
Hi Chitrita,
Please copy-paste the exact error and the command line in both cases
(working and not working). Also, what platform are you working on? Did
you by chance edit the .mdp file under windows?
Cheers,
Tsjerk
On Sat, Oct 11, 2008 at 6:46 PM, Chitrita Dutta Roy
<[EMAIL PROTECTED]> wrote:
I want to perform MD Equilibration run under position restrained for
200ps. Bond
distances were constrained using the LINCS (Linear Constraints) algorithm,
the water molecules were restrained using the SETTLE algorithm. In order to
do this I have modified nsteps in original pr.mdp file. Following i
Martin Höfling wrote:
Am Samstag, 11. Oktober 2008 schrieb Lee Soin:
The command grompp used to have options -shuffle, -sort and -np, but it
seems that they appear no more with version 4.0?
These options were used for particle decomposition in the tpr file. Gromacs 4
default method is domain
Lee Soin wrote:
This seems to me a very complicated realization. Why doesn't
GROMACS provide an easy way for wall simulation?
How about reading manual section 7.3.20 "Walls" in the Gromacs-4.0 manual? I
think that would be what you're after.
-Justin
2008/10/11 Omer Markovitch <[EMAIL
Am Samstag, 11. Oktober 2008 schrieb Lee Soin:
> The command grompp used to have options -shuffle, -sort and -np, but it
> seems that they appear no more with version 4.0?
These options were used for particle decomposition in the tpr file. Gromacs 4
default method is domain decomposition, but as
This seems to me a very complicated realization. Why doesn't GROMACS provide
an easy way for wall simulation?
2008/10/11 Omer Markovitch <[EMAIL PROTECTED]>
> Oh, I didn't read carefully.
> My suggestion would be, perhaps, to physically put atoms on the sides of
> the box (possibly, fill each sid
The command grompp used to have options -shuffle, -sort and -np, but it
seems that they appear no more with version 4.0?
--
Sun Li
Department of Physics
Nanjing University, China
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org
Ravi,
Just come to terms with PBC: the box has no outside. Chapter 3 of the manual...
Tsjerk
On Sat, Oct 11, 2008 at 1:30 PM, ravi sharma <[EMAIL PROTECTED]> wrote:
> So how could i do this energy conservation,
>
>
> Ravi Datta Sharma
> Lecturer,
> Bioinformatics,
> Department of Microbiology,
>
So how could i do this energy conservation,
Ravi Datta Sharma Lecturer, Bioinformatics,
Department of Microbiology,
CCS Unversity,
Meerut
--- On Sat, 11/10/08, sudheer babu <[EMAIL PROTECTED]> wrote:
From: sudheer babu <[EMAIL PROTECT
Oh...Similar type of problem once I have got, so got reply from some
one in archives that if use comm_grps= protein , protein will not come
out of the water box.So thats why I have suggested, If I say wrong
answer regret for that
>* Hi,
*>* Ravi
*>* Use comm_grps = protein in your .mdp file.
*>
sudheer babu wrote:
Hi,
Ravi
Use comm_grps = protein in your .mdp file.
3. protein coming out of the box (ravi sharma)
No!
You will ruin energy conservation...
Hello everyone
my protein coming out of the box in final md how can i fix my
protein in the middle of
Hi,
Ravi
Use comm_grps = protein in your .mdp file.
>
> 3. protein coming out of the box (ravi sharma)
>
>
> Hello everyone
>
> my protein coming out of the box in final md how can i fix my protein in
> the middle of the box. can you help me out??
>
>
>
___
1021 results for "protein out box" on the gromacs search page (mailing
list search). The first so many are relevant. Why not checking the
archives first? Oh, and it's mentioned in the wiki too.
Tsjerk
On Sat, Oct 11, 2008 at 11:03 AM, ravi sharma <[EMAIL PROTECTED]> wrote:
>
> Hello everyone
>
>
On a related note, I remember reading a paper recently, where they take
a few shells of water molecules with full atomicity, but "continuum"
beyond that. They also took care about the exchange between the
"molecular" water shell and the continuum as the polymer/protein
conformation changes during t
Hello everyone
my protein coming out of the box in final md how can i fix my protein in the
middle of the box. can you help me out??
Thanks
Ravi Datta Sharma Lecturer, Bioinformatics,
Department of Microbiology,
CCS Unversity,
Meerut
Hi Art,
You could, but should you? What do you think to gain? One layer of
water is approximately 2.5 A, so with 6 you'd have about two layers of
water 'free'. With position restraints on the rest, you'd still be
calculating all forces and such, so there's not much gain there. On
top of that, the
Oh, I didn't read carefully.
My suggestion would be, perhaps, to physically put atoms on the sides of the
box (possibly, fill each side completely), and to place on them very high
repulsion.
You might want to freeze them up, and exclude their self interactions from
the energy calculation.
Good gue
Possibly what he is interested in is a system WITHOUT PBC? I don't think
with PBC the system is really "confined", since there is no true wall to
reflect the colliding molecules. Thus to study the effect of real
confinement, it is necessary to remove PBC and impose reflective
boundary conditions. I
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