Dear all,
i'm sorry for confusion in last mail... i wrote that i did gmxcheck, and
pasted results of gmxdump...
here are results from gmxcheck
Checking file traj.trr
trn version: ---
Program gmxcheck, VERSION 3.3.1
Source code file: ../.
Many thanks, Dallas!
J. Zhang
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Dallas B. Warren
Sent: Friday, 21 July 2006 2:23 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] RE: g_h2order
As implied by the manual entry for this analy
As implied by the manual entry for this analysis tool, the mu ones are
dipole moments.
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
Dear Gromacs users,
When I use
g_h2order -f traj.xtc -n index.ndx -s XXX.tpr -d Z -o order.xvg
to analyze the orientation of water molecules with respect to the normal
in Z direction, I found there are 5 columns in order.xvg. They are
xaxis label "box (nm)"
yaxis label "mu_x, mu_y, mu_z (
>I would start a dynamical study with DPC micelles and peptides, but the
DPC is not
>mentioned in topology database.I imported the dpc.itp file in
/usr/local/gromacs/share/gromacs/top/ ,
> but this is not enough: in fact, when I start converting the pdb file,
I find the error "DPC
>not found in re
Solution may be to center the aggregates that are interacting into the
center of the box, and for the entire trajectory too.
But that doesn't work well if you have a lot of aggregates running
around.
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victo
All,
Is there any way to automatically generate a topology file containing
all of the parameters that normally would come from the force field?
For example, filling in each bond in the [ bonds ] section with
explicit parameters that would instead usually come from the included
force field file wh
Dear all,
I'm setting up some relative free energy calculations involving
changing atom types, and I have a related question about topologies.
In the dihedrals section, if my force field contains parameters for
the dihedral states organized by bond type, these are automatically
filled in when n
Hi Amit,
Begin forwarded message:
From: [EMAIL PROTECTED]
Date: July 20, 2006 5:03:34 PM EDT
To: "Pradip Kumar Biswas" <[EMAIL PROTECTED]>
Subject: QMMM simulation
Dear Sir,
While running mdrun for normal MD for the system at 300K, I am getting
following error
"ODIIS| Insufficient progress; res
Dear GMX users,
Recently i installed gromacs-3.3.1 on IBM powerpc64 with mpi support.
some of the details of the machines are as follows:
---
hostname = cnode39
uname -m = ppc64
uname -r = 2.6.5-7.139-pseries64
uname -s = Linux
/bin/arch= ppc64
---
Hi
for all ...Can somebody help me,?
for
make a bonded interaction betweenHIS an Zinc atom (in protein
with HIS redisidues make bond with a Zn atom by its NE2 atoms)
I
need edit some files ../topfirst I need modify ffgmxbon.itp
The
references about FE NR5 is only example ..
priyanka srivastava wrote:
Dear Sir,
thank you so much for your reply.
I made the index.ndx file and ran grompp with the
index file that I have made, but with no change and I
still get the same mesg.
I just hope I have understood your suggestion
correctly. Which manual sorting are we talking abo
On 7/20/06,
[EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:From: priyanka srivastava <
[EMAIL PROTECTED]>Subject: [gmx-users] atom names do not matchThanks again for your kind response.I guess I will write down my problem once again :-)
Warning: atom names in 96_neatsys14.top and test.grodon't mat
Dear Sir,
thank you so much for your reply.
I made the index.ndx file and ran grompp with the
index file that I have made, but with no change and I
still get the same mesg.
I just hope I have understood your suggestion
correctly. Which manual sorting are we talking about?
What exactly is the probl
priyanka srivastava wrote:
Thanks again for your kind response.
I guess I will write down my problem once again :-)
I am trying to study a pure bilayer system for which I
am interested in running the production run using
gromacs. I already have the system with me i.e. a pdb
file after the mini
Thanks again for your kind response.
I guess I will write down my problem once again :-)
I am trying to study a pure bilayer system for which I
am interested in running the production run using
gromacs. I already have the system with me i.e. a pdb
file after the minimization and all the constrai
On Thu, 2006-07-20 at 14:55 +0200, Berk Hess wrote:
>
>
> >From: Dongsheng Zhang <[EMAIL PROTECTED]>
> >Reply-To: Discussion list for GROMACS users
> >To: Discussion list for GROMACS users
> >Subject: RE: [gmx-users] segmentation fault, very high KE but no high
> >velocity
> >Date: Thu, 20 Jul
From: Dongsheng Zhang <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] segmentation fault, very high KE but no high
velocity
Date: Thu, 20 Jul 2006 08:51:43 -0400
Dear Berk,
Thank you for your reply. The veloci
Dear Berk,
Thank you for your reply. The velocities are from trr file. Could you
please tell me what those values are (for t-dt/2 or t+dt/2 or t)? If
they are not for time step t, could you change the source code to output
the value for t to keep consistency with KE? By the way, I had set
nstfout
From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] confused about rcoulomb<=rlist
Date: Thu, 20 Jul 2006 14:18:19 +0200
Berk Hess wrote:
So I will implement this for Gromacs 4.0.
The o
Hi,
i have done recently some benchmark runs on some new testsystems:
New machines are a woodcrest based and an opteron dualcore from sun.
If i have money today, i would buy a woodcrest based cluster ...
Greetings,
Florian
--
--
Berk Hess wrote:
So I will implement this for Gromacs 4.0.
The only, technical, detail is if one would want to determine
beta with rcoulomb or with rcoulomb_switch,
as the real space part will start deviating from rcoulomb_switch.
But I would prefer rcoulomb for consistency reasons.
I have
Hi all,
I am studying the fusion of small aggregates that can occur near the
crossover point of my PBC. So for measuring distances between two of
these objects I have defined 2 groups, each containing several
monomers. Each time a monomer crosses the wall of the box, g_dist does
not consi
So I will implement this for Gromacs 4.0.
The only, technical, detail is if one would want to determine
beta with rcoulomb or with rcoulomb_switch,
as the real space part will start deviating from rcoulomb_switch.
But I would prefer rcoulomb for consistency reasons.
I have committed the new
Hi
This isn't much information, but I guess, those problems may occur due
to the termini (and their missing FF-entries(?)) of the DNA.
At first, you should have a look at the top-file and find out, which
bases/atoms are responsible for the warnings. Then have a look, if the
dihedral simply isn
Isabella Daidone wrote:
Hi,
this is what is written in one of the options in editconf:
" -[no]c bool no Center molecule in box (implied by -box and -d)".
Moreover, in the mailing list you can find discussion about this topic
with version 3.2 and David said it was a bug (that -d -c did no
On Thu, 20 Jul 2006 10:24:25 +0200 (CEST)
Isabella Daidone <[EMAIL PROTECTED]> wrote:
Hi,
this is what is written in one of the options in
editconf:
" -[no]c bool no Center molecule in box (implied
by -box and -d)".
Now you mention it !
did you try a two step process: 1) center (-c),
Hi,
this is what is written in one of the options in editconf:
" -[no]c bool no Center molecule in box (implied by -box and -d)".
Moreover, in the mailing list you can find discussion about this topic
with version 3.2 and David said it was a bug (that -d -c did not really
center).
So I w
HI Isabelle,
I try again, just to know if it is not true that -d
implies centering...
Hi,
when using editconf -d with gromacs version 3.3, it
seems that the protein is
not at the center but at the corner of the box.
In gromacs version 3.3, does option -d in editconf
really imply that th
I try again, just to know if it is not true that -d implies centering...
Hi,
when using editconf -d with gromacs version 3.3, it seems that the protein is
not at the center but at the corner of the box.
In gromacs version 3.3, does option -d in editconf really imply that the
protein will be c
mario ciappy <[EMAIL PROTECTED]> ha scritto: Hello everyone,I would start a dynamical study with DPC micelles and peptides, but the DPC is not mentioned in topology database.I imported the dpc.itp file in /usr/local/gromacs/share/gromacs/top/ , but this is not enough: in fact, when I start c
mario ciappy <[EMAIL PROTECTED]> ha scritto: Hello everyone,I would start a dynamical study with DPC micelles and peptides, but the DPC is not mentioned in topology database.I imported the dpc.itp file in /usr/local/gromacs/share/gromacs/top/ , but this is not enough: in fact, when I start c
mario ciappy <[EMAIL PROTECTED]> ha scritto: Hello everyone,I would start a dynamical study with DPC micelles and peptides, but the DPC is not mentioned in topology database.I imported the dpc.itp file in /usr/local/gromacs/share/gromacs/top/ , but this is not enough: in fact, when I start c
From: Dongsheng Zhang <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: [gmx-users] segmentation fault, very high KE but no high velocity
Date: Wed, 19 Jul 2006 12:53:00 -0400
Hello, gmx users,
I got segmentation fault during a s
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