David Mobley wrote:
I have further replica exchange questions...
The order is that from low temperature to high temperature (as you could
check from the edr files) and when swaps happen the coordinates and
boxes are exchanged between CPUs.
OK. In other words the replicas are always ordered by
abhishek sharma wrote:
sir,
i want to introduce a shell model in ZnS particles and have the
potential data. I gone through your Novel Shell Model for the water
molecule givem in the /share/top as sw.itp.
could you please help me out how I can introduce all these potentials
in my model
From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: "Discussion list for GROMACS users"
Subject: Re: [gmx-users] replica exchange output information
Date: Mon, 7 Jan 2008 10:40:44 -0800
David,
> The order is that from low temperature to high temperature
David van der Spoel wrote:
David Mobley wrote:
It would be nice to have this sort of information (i.e. that demux.pl
exists, and what it does) in the documentation or on the REMD page of
the wiki.
I've tried to write a bit about it:
http://wiki.gromacs.org/index.php/REMD#Post-processing
Than
Hi all,
sorry for the previous wrong links (Thanks to Mark):
http://www.gromacs.org/pipermail/gmx-users/2002-April/001333.html
http://www.gromacs.org/pipermail/gmx-users/2002-March/001000.html
http://www.gromacs.org/pipermail/gmx-users/2006-July/022999.html
Regards,
andrea
andrea spitaleri w
Dear all Gromacs users:
I want to obtain demux.pl for analysis REMD, but I do not know how to get
it, please help me!
Thank you very much!
-
雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___
gmx-users mailing listgmx-users@groma
xi zhao wrote:
> Dear all Gromacs users:
> I want to obtain demux.pl for analysis REMD, but I do not know how to
> get it, please help me!
> Thank you very much!
As David van der Spoel said here just today
http://www.gromacs.org/pipermail/gmx-users/2008-January/031570.html, and
as is noted on th
Hi Swapna,
The PRODRG server generates topologies for the gmx force field (ffgmx;
deprecated!). You most likely want to have a topology compliant with the
Gromos96 force fields (e.g. ffG43a2). For this you need to use the beta
version of the PRODRG server.
Mind you that force field parameterizati
Hi,
I am doing the Kerrigan Drug-enzyme tutorial.
I could generate the drg.itp, drg.gro files using PRODRG server.
When I use the grompp step before the energy minimization I encounter a
problem
A fatal error was shown: atom types CB, CR61 and OS were not found.
--
Quoting SWAPNA <[EMAIL PROTECTED]>:
> Hi,
> I am doing the Kerrigan Drug-enzyme tutorial.
> I could generate the drg.itp, drg.gro files using PRODRG server.
> When I use the grompp step before the energy minimization I encounter a
> problem
>
> A fatal error was sh
Hi Mitra,
You can add it in the file FF.dat in the $GMXDIR/share/gromacs/top/
directory.
Cheers,
Tsjerk
On Jan 8, 2008 3:35 PM, Mitra Kheirabadi <[EMAIL PROTECTED]> wrote:
> Dear Dr. Smith
>
> I want to run a virus phosphorylated protein by gromacs. Furtunatly, you
> construct related force fi
Dear Dr. Smith
I want to run a virus phosphorylated protein by gromacs. Furtunatly, you
construct related force field by ffG43A1p name. I copied this force field to
top. file gromacs but when I constructed pdbgmx, there is no any ffG43a1p to
select. Could you help me?
I be so grateful t
Hi All,
In December here was a short discussion about a water system, for which
gromacs versions 3.2.1 and 3.3.1 produced different average volumes. I
have experienced similar thing with Marrink's coarse grained water
(about 1500 beads in the box), but to opposite direction.
My test runs wit
On Tue, 8 Jan 2008 06:35:28 -0800 (PST)
Mitra Kheirabadi <[EMAIL PROTECTED]> wrote:
Dear Dr. Smith
I want to run a virus phosphorylated protein by gromacs. Furtunatly, you
construct related force field by ffG43A1p name. I copied this force field to
top. file gromacs but when I constructed
Dear Periola
I appreciate your kindly help.
Respectfully
Xavier Periole <[EMAIL PROTECTED]> wrote:
On Tue, 8 Jan 2008 06:35:28 -0800 (PST)
Mitra Kheirabadi wrote:
> Dear Dr. Smith
>
> I want to run a virus phosphorylated protein by gromacs. Furtunatly, you
>construct related force
On Tue, 8 Jan 2008 15:39:51 +0200 (EET)
Perttu Niemela <[EMAIL PROTECTED]> wrote:
Hi All,
In December here was a short discussion about a water system, for which
gromacs versions 3.2.1 and 3.3.1 produced different average volumes. I have
experienced similar thing with Marrink's coarse grained
Dear Wassenaar
I appreciate your kindly help.
Respectffuly
Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
Hi Mitra,
You can add it in the file FF.dat in the $GMXDIR/share/gromacs/top/ directory.
Cheers,
Tsjerk
On Jan 8, 2008 3:35 PM, Mitra Kheirabadi < [EMAIL PROTECTED]> wrote:
Hi gromacs users
For my work I have performed some simulations of a protein in water with an
other MD software not compatible with GROMACS. And I would like to compute the
time evolution of the secondary structure of my protein, I know that the
do_dssp tool in GROMACS is made for this. This too
Dear Dr.Periole
I add ffG43a1p to FF.dat/ top and changed 11 to 12 on this file but sorry
again I did not appear. please help me.
Respectfully
Mitra Kheirabadi <[EMAIL PROTECTED]> wrote:
Dear Periola
I appreciate your kindly help.
Respectfully
Xavier Periole <[EMAIL P
Dear all,
When using the g_density tool am I calculating the density of a group of
molecules in respect to the atoms or to the center of mass of these molecules?
Thank you for your help
Antonia
__
Sent from Yahoo! Mail - a smarter
Hi,
Could anyone tell me how to parameterize a new molecule for using it with
OPLS (basic principles). What a .pdb file should look like and what .mdp
variables are specificaly related to OPLS?
Thank you in advance
Egidijus
-
Never miss a thi
Atoms.
- Original Message
From: Antonia Vyrkou <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Tuesday, January 8, 2008 4:05:26 PM
Subject: [gmx-users] g_density
Dear all,
When using the g_density tool am I calculating the density of a group of
molecules in respect to the atoms
van Bemmelen wrote:
Hi guys,
I noticed that at this moment the mailing list search on the GROMACS
website only gives results from before some date in May 2007. So it
seems to me that the search database hasn't been updated since then. Is
this done on purpose or is something wrong?
For gmx-users
Hi guys,
I noticed that at this moment the mailing list search on the GROMACS
website only gives results from before some date in May 2007. So it
seems to me that the search database hasn't been updated since then. Is
this done on purpose or is something wrong?
For gmx-users there is a way around
Egidijus Kuprusevicius wrote:
Hi,
Could anyone tell me how to parameterize a new molecule for using it
with OPLS (basic principles).
See http://wiki.gromacs.org/index.php/Parameterization
> What a .pdb file should look like
As normal, you need atom and residue names corresponding to those f
Mitra Kheirabadi wrote:
Dear Dr.Periole
I add ffG43a1p to FF.dat/ top and changed 11 to 12 on this file but
sorry again I did not appear. please help me.
The new forcefield files have to go to the same location as the old
ones, in the subdirectory something like share/gromacs/top. Or
prefe
Tandia, Adama wrote:
Dear FOLKS,
Is a standard protocol to add new force field into Gromacs
developed/published somewhere?
Yes and no. The format required is well described in Chapter 5 of the
GROMACS manual, and anyone wishing to add a new forcefield can do so by
using the knowledge there
ABEL Stephane 175950 wrote:
Hi gromacs users
For my work I have performed some simulations of a protein in water with an
other MD software not compatible with GROMACS. And I would like to compute the
time evolution of the secondary structure of my protein, I know that the
do_dssp tool in GROM
Dear FOLKS,
Is a standard protocol to add new force field into Gromacs
developed/published somewhere? I have great interest in Embedded Atom
Method, Modified EAM and Stillinger-Weber force field. These are force
fields, I believe, that could help in a great deal the glass/ceramics
community! Same
Sorry, but in source of v3.3.2 and 3.3.1 of the website , there is not
demux.pl
script, please help me!
Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote:
> Dear all Gromacs users:
> I want to obtain demux.pl for analysis REMD, but I do not know how to
> get it, please help me!
> Thank you v
Hi Mark
I read the manual and I used umabrella sampling and I got a curve for pmf but
now I want pmf by energy perturbation that I want to sure about my curve that I
got by umbrella sampling.
my question is about .itp file and how do I create.
thank you very much.
---
Hi Mark
I read the manual and I used umabrella sampling and I got a curve for pmf but
now I want pmf by energy perturbation that I want to sure about my curve that I
got by umbrella sampling.
my question is about .itp file and how do I create.
thank you very much.
[EMAIL PROTECTED] wrote: The re
Hi Mark
I read the manual and I used umabrella sampling and I got a curve for pmf but
now I want pmf by energy perturbation that I want to sure about my curve that I
got by umbrella sampling.
my question is about .itp file and how do I create.
thank you very much.
[EMAIL PROTECTED] wrote: The re
Hi Mark
I read the manual and I used umabrella sampling and I got a curve for pmf but
now I want to calculate pmf by energy perturbation that I want to sure about my
curve that I got by umbrella sampling.
my question is about .itp file and how do I create.
thank you very much.
[EMAIL PROTECTED]
xi zhao wrote:
Sorry, but in source of v3.3.2 and 3.3.1 of the website , there is not
demux.pl
src/contrib/scripts
script, please help me!
*/Mark Abraham <[EMAIL PROTECTED]>/* ??:
xi zhao wrote:
> Dear all Gromacs users:
> I want to obtain demux.pl for analysis REMD, but I do
Mark Abraham wrote:
Egidijus Kuprusevicius wrote:
Hi,
Could anyone tell me how to parameterize a new molecule for using it
with OPLS (basic principles).
See http://wiki.gromacs.org/index.php/Parameterization
> What a .pdb file should look like
As normal, you need atom and residue names co
David van der Spoel wrote:
xi zhao wrote:
Sorry, but in source of v3.3.2 and 3.3.1 of the website , there is
not demux.pl
src/contrib/scripts
Actually, Xi Zhao is right here, David. Neither of the 3.3.1 or 3.3.2
source distributions has either this subdirectory or demux.pl anywhere else.
Mark Abraham wrote:
David van der Spoel wrote:
xi zhao wrote:
Sorry, but in source of v3.3.2 and 3.3.1 of the website , there is
not demux.pl
src/contrib/scripts
You're dead right.
WIll fix this for the next release. It is attached to this mail.
Actually, Xi Zhao is right here, David. N
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