Cherry Y. Yates wrote:
Dear Gromacs users and developers,
I am studying a system consisting of six molecules (3 groups). I would like to
keep the center-of-mass motion of each molecule with the system having zero
center-of-mass motion. So I set comm_mode=Linear. In the simulation,
immediately th
I am sorry, Mark. I didn't mean to make you feel bad.
But I'll keep what you said in mind.
Thank you.
Sanghwa Han
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Mark Abraham
Sent: Wednesday, January 17, 2007 3:45 PM
To: Discussion list for GROMACS users
S
한상화 wrote:
> Thank you Mark.
> The method you suggest is exactly what I tried.
> I prepared a structure of two molecules in which the S...S distance was
> made to be 0.206 nm (this value is within the tolerance).
> But when I ran pdb2gmx -ignh -ss, it only asked me to form intramolecular
> disulfid
Thank you Mark.
The method you suggest is exactly what I tried.
I prepared a structure of two molecules in which the S...S distance was
made to be 0.206 nm (this value is within the tolerance).
But when I ran pdb2gmx -ignh -ss, it only asked me to form intramolecular
disulfides. It did not ask for
한상화 wrote:
> Dear Mark,
> Could you kindly tell me how it can be done?
The general procedure is to get a structure with the relevant S atoms
close enough together, then use pdb2gmx -ss on that structure (possibly
with -ignh too). You may need to copy specbond.dat from the library to
your working d
Dear Mark,
Could you kindly tell me how it can be done?
Or tell me where in the manual to look up?
What I am trying to do is either generating a new residue CysS-SG (named
CYG, for example) or forming a disulfide between CysSH and GSH during
running Gromacs (I am not sure if there is a command or f
한상화 wrote:
> Dear all,
>
>
>
> Is there any way to make a disulfide between protein CysSH and GSH? Or
> an interchain disulfide?
Yes
Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please d
Dear all,
Is there any way to make a disulfide between protein CysSH and GSH? Or an
interchain disulfide?
I am interested in running MD for Protein-S-SG (i.e. glutathiolated
protein).
Thanks
Sanghwa Han
___
gmx-users mailing listgmx-user
Dear Gromacs users and developers,
I am studying a system consisting of six molecules (3 groups). I would like to
keep the center-of-mass motion of each molecule with the system having zero
center-of-mass motion. So I set comm_mode=Linear. In the simulation,
immediately the center-of-mass motion o
Sunny wrote:
Hi,
Continue to the energy minimization problem. I use l-bfgs to run the
energy minimization for the structure summarized in the previous message
below. The em output topology confout.gro doesn't contain velocity data.
Then, I try to convert confout.gro into .pdb format by:
As
Arrgh.
Correct procedure is
1) Get source code
2) Install prerequisites
3) Decide on a location from which to install, I'll call this
/source/dir - this should be in user space
3) Decide on a location into which to install, I'll call this /dest/dir
- this can be anywhere, but you need root acc
Hi Sunny,
With energy minimization there are no velocities.
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
Hi,
Continue to the energy minimization problem. I use l-bfgs to run the energy
minimization for the structure summarized in the previous message below. The
em output topology confout.gro doesn't contain velocity data. Then, I try to
convert confout.gro into .pdb format by:
editconf -f confo
* Ansgar Esztermann <[EMAIL PROTECTED]> [Tue, 16 Jan 2007 18:12:40 +0100]:
On Tue, Jan 16, 2007 at 07:42:52PM +0300, Vladimir Korostelev wrote:
> I do not have it! I used:
> ./configure --prefix=/home/vladimir/gromacs-3.3.1
>
> but there is not bin there. It sounds hell but it's true ~:-0
> I thi
On Tue, Jan 16, 2007 at 07:42:52PM +0300, Vladimir Korostelev wrote:
> I do not have it! I used:
> ./configure --prefix=/home/vladimir/gromacs-3.3.1
>
> but there is not bin there. It sounds hell but it's true ~:-0
> I think my binaries are in /home/vladimir/gromacs-3.3.1/src/kernel
>
There are
Vladimir Korostelev wrote:
* Robert fiske <[EMAIL PROTECTED]> [Tue, 16 Jan 2007 12:09:14 -0500]:
>but there is not bin there. It sounds hell but it's true ~:-0
>I think my binaries are in /home/vladimir/gromacs-3.3.1/src/kernel
Out of curiosity did you run "make install" after make?
fiske
Y
Yes, I used:
$ ./configure --prefix=/home/vladimir/gromacs-3.1.1
$ make
$ make -n install
Just checked the man page for make, and the -n option seems to tell make to
just show output of what it would have done, but doesn't actually do the
install, so try running make install without the -n
Robert Johnson wrote:
Hello everyone,
I'm using the current development version of Gromacs to perform
replica exchange MD. Are there any Gromacs tools to aid in the
analysis of the trajectories. For example, are there tools that enable
trajectories grouped by temperature? Is there a way to determ
* Robert fiske <[EMAIL PROTECTED]> [Tue, 16 Jan 2007 12:09:14 -0500]:
>but there is not bin there. It sounds hell but it's true ~:-0
>I think my binaries are in /home/vladimir/gromacs-3.3.1/src/kernel
Out of curiosity did you run "make install" after make?
fiske
Yes, I used:
$ ./configure -
Hello everyone,
I'm using the current development version of Gromacs to perform
replica exchange MD. Are there any Gromacs tools to aid in the
analysis of the trajectories. For example, are there tools that enable
trajectories grouped by temperature? Is there a way to determine the
temperature of
but there is not bin there. It sounds hell but it's true ~:-0
I think my binaries are in /home/vladimir/gromacs-3.3.1/src/kernel
Out of curiosity did you run "make install" after make?
fiske
_
From photos to predictions, The MSN
* Tsjerk Wassenaar <[EMAIL PROTECTED]> [Tue, 16 Jan 2007 16:35:19
+0100]:
Hi Vladimir,
It should also be in the directory which you fed to ./configure with
the option --prefix=
There, there should be a directory bin/ which contains all the
binaries.
I do not have it! I used:
./configure --pref
I guess you misunderstood that.
What you have there, is the terminal hydrogen, which is an hydroxyl one
and therefore fully ok.
You should search for an atom at the nucleobase, which has atom type 25.
This usually has to be changed. Strange error, though :)
I think its somewhere around N1 for g
Hi Vladimir,
It should also be in the directory which you fed to ./configure with
the option --prefix=
There, there should be a directory bin/ which contains all the
binaries. In addition, it contains a script GMXRC, which you can use
to set all the environment variables properly, including the P
Hi Tsjerk,
The system has 1 protein (118 atoms) and 256 DPPC lipids (12800 atoms)
without solvent. The box size is 6.125, 12.5, 9.5 nm. The make_ndx output is
as follows. I can run l-bfgs on the structure.
Analysing residue names:
Opening library file
/usr/local/packages/gromacs/g_3.3.1/shar
Sending a message again, won't help you, if you don't follow the Marks'
suggestions.
And please, not again a discussion about politeness...;)
This is, what he wrote:
hi everyone
> I need to pull the two parallel monolayers together,the two monolayers
> are in the x-y plane , so i pull the one
Thanks for help with GROMACS installation.
I have installed GROMACS and it seems successfully because ./luck has
brought
a quote this time (gcq#119 "Bring Out of Gimp" (Pulp Fiction))!
However my attempt to run demo in /tutor subdirectory has failed - a
window popped
up with a message 'pdb2gm
Hi George,
You didn't mention whether this was with or without solvent. This is
probably due to an error in your starting structure, and I advice to
check it carefully. Also, if you're running in solvent, check your
box.
Step= 57, Dmax= 4.3e-03 nm, Epot= -1.79963e+23 Fmax= inf, atom=
Sunny wrote:
Hi,
I have the following error when running energy minimization
(integrator=steep):
(similar message occurs serveral times in previous steps as for Step 57)
... ... ... ...
I'd like to know if there is any method to let this EM run.
Probably the problem is with your starting st
Hi,
I have the following error when running energy minimization
(integrator=steep):
(similar message occurs serveral times in previous steps as for Step 57)
... ... ... ...
Step 57, time 0.114 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 110.960770 (between atoms 1576 and
Tsjerk Wassenaar wrote:
Vladimir,
The default "--prefix" is /usr/local. You're not allowed to write
there as user, that's why that failed. So it did succeed as root; root
is allowed to write there. I suggest installing as user, with
./configure --prefix=/home/vladimir/gmx331 and whatever other o
Dear Drs. Martin Hofling and Mark Abraham,
I agree with your suggestions since I have gone through the gmx_users previous
mails written by others in this line where in compilation on SGI machines
didnot go off without problems. In any case I would like to bring to yo
Vladimir,
The default "--prefix" is /usr/local. You're not allowed to write
there as user, that's why that failed. So it did succeed as root; root
is allowed to write there. I suggest installing as user, with
./configure --prefix=/home/vladimir/gmx331 and whatever other options
you need. Check ./
Vladimir Korostelev wrote:
* Mark Abraham <[EMAIL PROTECTED]> [Tue, 16 Jan 2007 20:43:56 +1100]:
Until you know what you're doing, I suggest following the
installation
instructions on the gromacs web page precisely.
I think I did! it was done in 3 simple steps:
$./configure
$make
$make in
* Mark Abraham <[EMAIL PROTECTED]> [Tue, 16 Jan 2007 20:43:56
+1100]:
Until you know what you're doing, I suggest following the
installation
instructions on the gromacs web page precisely.
I think I did! it was done in 3 simple steps:
$./configure
$make
$make install
after installation o
Vladimir Korostelev wrote:
Hello
I have installed GROMACS 3.3.1 for the first time and want to check
whether it was done
correct or not.
Until you know what you're doing, I suggest following the installation
instructions on the gromacs web page precisely.
There were no error messages dur
Hello
I have installed GROMACS 3.3.1 for the first time and want to check
whether it was done correct or not.
There were no error messages during installation and I wanted to check
whether it's correct or not by typing command:
$./luck
and there was error message something like 'Command not fo
Sivashangari Gnanasambandam wrote:
Hi,
I am trying to study the dissolution of urea in water. After adding the
water molecule using genbox, I did the energy minimization by applying
pbc. Then I run the equilibration for 300ps using NPT anisotropic
pressure coulpling and variable axis only in th
Am Dienstag, 16. Januar 2007 09:59 schrieb Mark Abraham:
> Unfortunately, we already know gromacs 3.3 tends to compile nicely with
> gcc on almost everything. I'd suggest putting gcc on the Octane system...
> if there's no binary distribution available, you can use the existing
> compilers to comp
From: Volker Knecht <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: gmx users
Subject: [gmx-users] epsilon_rf
Date: Fri, 12 Jan 2007 12:04:34 +0100
Dear GROMACS users,
in the past I tended to use PME to calculate electrostatic interactions,
but to be able to reach larg
>
>
>
>
>
> Dear Dr. Martin Hoefling,
> Thankyou for the reply.
> I have installed the gromacs 3.3 package on my PC with gcc compilers and I
> didnot get any such errors. I am using the package without any hitch. Any
> other information you would like me to give in this regard kindly let me
> know
Dear Dr. Martin Hoefling,
Thankyou for the reply.
I have installed the gromacs 3.3 package on my PC with gcc compilers and I
didnot get any such errors. I am using the package without any hitch. Any
other information you would like me to give in this regard kindly le
42 matches
Mail list logo
