Tcl is not part of Gromacs. Please direct your enquiry to the appropriate
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http://www.tcl.tk/community/
Andreas
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of varsha gautham
Sent: 20 January 2009 07:05
To: gmx-users@gromacs.org
Su
Mohammed Kamal wrote:
Tcoupl = berendsen
tau_t= 0.1 0.1 0.1 0.1
tc_grps = protein T27 SOL Cl ; T27 is the ligand
General advice: do not couple solvent and ions separately. I believe there is a
newer version of the tutorial that fixes
Hi,
I have a system with three kinds of particles. For this time I want to examine
possible clusters containing only two kinds of particles. My index file
consists of all
the numbers of those atoms which belong to the particles of interest.
Then
g_clustsize(402) -n index.ndx
It seems to work cor
Vitaly Chaban wrote:
Hi,
I have a system with three kinds of particles. For this time I want to examine
possible clusters containing only two kinds of particles. My index file
consists of all
the numbers of those atoms which belong to the particles of interest.
Then
g_clustsize(402) -n index.nd
> I just now started with TCL scripting.And it will be helpful if someone
> tell me how to write a TCL script for the following queries.?
> 2. what is the total charge of the protein?
Yeah, Tcl is a good way to write scripts for gromacs but it is really
not a part of the package. :)
As for th
Hi,
I am running stress simulations of vesicles and lipid bilayer
membranes, which work on one processor but fail when using multiple
processors. The simulations run Marrink's CGMD model with Gromacs
4.0.2 (sorry I am unable to upgrade until next week) on openmpi and
mpich. The simulation
Also check out "make_ndx -help". Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Mon, Jan 19, 2009 at 18:28, Vitaly Chaban wrote:
> > I am running a simulation of 5 time steps and am trying to avoid
> setting
> > nstxtcout
Hi,
This bug has been fixed in 4.0.3,
but I forgot about it when writing the release notes.
Berk
> From: ydub...@uvm.edu
> To: gmx-users@gromacs.org
> Date: Tue, 20 Jan 2009 08:53:15 -0500
> Subject: [gmx-users] deform option in parallel with Gromacs 4.0.2
>
> Hi,
>
> I am running stress simu
Dear users,
Does any one aware of how to carry out the simulations in presence of a
static and oscillating electric fields ? I found an option E_x, E_y, E_z
needed to be mentioned in the run mdp file. Other than this are there any
thing we need to mention ?
Ram.
__
> Source code file: matio.c, line: 533
>
> Fatal error:
> Lo: 0.00, Mid: 1.00, Hi: 1.00
>
>
> Although nclust.xvg, maxclust.xvg, avclust.xvg are created and seem
> adequate.
>
> However what could the above error indicate?
>that all atoms belong to the same cluster.
Yes, it's true
Vitaly Chaban wrote:
Source code file: matio.c, line: 533
Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00
Although nclust.xvg, maxclust.xvg, avclust.xvg are created and seem
adequate.
However what could the above error indicate?
that all atoms belong to the same cluster.
Yes, it's
Hi
I have checked the manual, but it did not help. Checking the cgnr column did
not help either.
What I do is just splitting the pdb file into two energy groups (chains A+B
and C). I do not change any definitions of charge groups in Gromacs.
As the result, I am getting "1996 and 1998 are in differe
Liu Shiyong wrote:
Hi
I have checked the manual, but it did not help. Checking the cgnr column
did not help either.
Well, did it indicate that these atoms are indeed in the same charge group? I
suggested before that you check out your topology to see how grompp is
interpreting it. If, as
>>
>> In other words, is information about the initial (in conf.gro)
>> numbering of molecules present in the xtc trajectory file? Looking at
>> the xtc using gmxdump I see the numbering always start with zero in
>> spite of the xtc-qrps arguments.
>>
> All files number from 0 to natom-1. You have
Hi all.
I have two machines with Intel Quad Core processors and Intel
motherboards. In the first one I'm running Open Suse with normal
partition scheme. In the second I'm running Ubuntu 8.04 with software
RAID 1.
Running a simulations in parallel (4 process, one for each core) in the
first
Am Dienstag, den 20.01.2009, 17:07 -0200 schrieb Alexandre Suman de
Araujo:
> I have two machines with Intel Quad Core processors and Intel
> motherboards. In the first one I'm running Open Suse with normal
> partition scheme. In the second I'm running Ubuntu 8.04 with software
> RAID 1.
Hard
Liu Shiyong wrote:
The problem lies here:
Including chain 1 in system: 1296 atoms 125 residues
Including chain 2 in system: 1274 atoms 123 residues
Including chain 3 in system: 2085 atoms 201 residues
This suggests that chain 2 (Protein B) should contain numbers up to about 2500.
Thanks.
I used the PDB file with H . It works though it's still a mystery for me
why PDB file without H couldn't work.
On Tue, Jan 20, 2009 at 1:53 PM, Justin A. Lemkul wrote:
>
>
> Liu Shiyong wrote:
>
>
>
> The problem lies here:
>
> Including chain 1 in system: 1296 atoms 125 residues
>
Liu Shiyong wrote:
Thanks.
I used the PDB file with H . It works though it's still a mystery for
me why PDB file without H couldn't work.
Because the atoms will be numbered wrong. When you use pdb2gmx, hydrogens will
be added to some groups (polar groups, aromatics, N-termini, etc). S
Hello all,
Is there anyway to provide constant velocity to any particular group of atoms.?
--
Avinash Kumar.
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Hi,
Is there any option to output total interaction energy
(without *internal
energy*) based on energy groups?
*g_energy -f r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr*
[shiy...@reco temp20090115]$ g_energy -f
r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr
Hi
Can we simulate "samlple putting on the equipment using GROMACS-MD package"?
Thank you
Lin
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gurgo> Hello all,
gurgo> Is there anyway to provide constant velocity to any particular group of
atoms.?
See acc-grps
===
Vitaly V. Chaban, Ph.D.(ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha..
> Is there any option to output total interaction energy
> (without *internal
> energy*) based on energy groups?
I don't know such. But it seems very easy to sum the terms which are
output.
===
Vitaly V. Chaban, Ph.D.(ABD)
School of Chemistry
V.N. Karazin Kha
Chih-Ying Lin wrote:
Hi
Can we simulate "samlple putting on the equipment using GROMACS-MD package"?
This question doesn't make any sense to me. If you can explain the procedure
you are interested in simulating, you might be able to get more useful advice.
-Justin
Thank you
Lin
Many thanks for Justin for your helpful comments, I think I still need your
help for the first question... I have included more details about my system
below
> Mohammed Kamal wrote:> > > Tcoupl = berendsen> > > > tau_t = 0.1 0.1 0.1 0.1>
> > > > tc_grps = protein T27 SOL Cl ; T27 is the
Mohammed Kamal wrote:
Many thanks for Justin for your helpful comments, I think I still need
your help for the first question... I have included more details about
my system below
> Mohammed Kamal wrote:
>
> > Tcoupl = berendsen
> >
> > tau_t = 0.1 0.1 0.1 0.1
> >
> > tc_grps =
Is it just me, or is it down at the moment? Trying to get the latest
version source files.
Catch ya,
Dallas Warren
A polar bear is a rectangular bear that has undergone a polar
transformation
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htt
Sorry seems that it was just me, or it is back up. Either way things
are good now.
Catch ya,
Dallas Warren
A polar bear is a rectangular bear that has undergone a polar
transformation
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