> Date: Wed, 1 Apr 2009 14:15:05 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Energy Conservation with 4fs timestep
>
> Joe Joe wrote:
> > Hi,
> >
> > I get good conservation when running NVE in gromacs with 4 fs when I use
> > PME-switch for el
I wanted the OPLS-UA because my system is large (3 proteins with 2 organic
molecules, in water), and, if the G43a1 forcefield gives me a MD speed of 70
ps/day, an all atom model will result much slower. So what else can I do to
speed up my MD, to get results in 1-3 months?.
Mensaje citado por David
Did you try g_angle??
Antonia
Date: Wed, 1 Apr 2009 11:35:29 +0530
From: venkat...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] How to calculate the dihedral angle variations ???
Hi Everyone !
How can i see the variations in the "Cβ-S-S-Cβ"
(Disulfide bridge) dihedral angle during
First of all Thanks for ur reply !
I tried both g_angle and g_chi with all suitable options, but i didn't get
the required result.Can u plz help me in this regard ???
2009/4/1 Antonia V.
>
> Did you try g_angle??
>
> Antonia
> --
> Date: Wed, 1 Apr 2009 11:35:29 +0530
Hello,
I am trying to simulate a system at the NVT ensemble, but after a few steps I
get the error
[compute-0-4:01361] *** Process received signal ***
[compute-0-4:01361] Signal: Segmentation fault (11)
[compute-0-4:01361] Signal code: Address not mapped (1)
[compute-0-4:01361] Failing at addre
Hi Venkat,
What exactly do you mean with variations. Do you want to follow the
angle over time, or do you want distributions with mean and variance
estimates? g_angle and g_chi seem to be the appropriate tools. You
mention you tried all suitable options, but fail to explain what you
tried and what
Hai Sir !
Actually i want to see the dihedral angle (Cβ-S-S-Cβ) variation over time.I
used the commands
"g_angle -f trajout.xtc -s gp123_b4full.tpr -n angle.ndx -od angdist.xvg -ov
angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oc dihcorr.xvg -type
dihedral -all"
"g_chi -s gp123_full.gro -f gp123
Antonia V. wrote:
Hello,
I am trying to simulate a system at the NVT ensemble, but after a few
steps I get the error
[compute-0-4:01361] *** Process received signal ***
[compute-0-4:01361] Signal: Segmentation fault (11)
[compute-0-4:01361] Signal code: Address not mapped (1)
[compute-0-4:01
Hi,
we performed for comparison pentadecane simulations using both the
4.0.2 version and 4.0.3, with the same mdp file (see below). Results
look quite different (reproducible), for 4.0.2 the system quickly (few
100 ps) enters the crystalline phase while it stays fluid for 4.0.3
(with an i
Hi again
I don't know if you were aware of it, but I have commented some Justin's
questions further down in the e-mail (my last e-mail wasn't only a
thank-email). Since it took so long, and other similar discussions are
still running I thought you have missed my comments (see below).
Now we h
Justin A. Lemkul wrote:
Edvin Erdtman wrote:
Hi again
I don't know if you were aware of it, but I have commented some
Justin's questions further down in the e-mail (my last e-mail wasn't
only a thank-email). Since it took so long, and other similar
discussions are still running I thought
Hi,
The release notes for 4.0.3 are at:
http://www.gromacs.org/content/view/181/132/
I don't see any relevant bug fixes there and I don't recall any either.
Please update to 4.0.4, since many small bugs have been fixed.
Berk
> From: rai...@bioinformatik.uni-saarland.de
> To: gmx-users@gromacs.
Dear List,
In the paper entitled "A new GROMOS force field for hexopyranose-based
carbohydrates" Journal of Computational Chemistry Volume 26 Issue 13,
Pages 1400 - 1412. When the authors ran unrestrained md for 2ns, once
the conformation is stabilised in chair, they donot observe any
further tran
Hi
We have tried with no cutoff, as I have written in former emails, but
that was when we got trouble with LINCS warnings. We then thought that
we could try to continue remove lipids in the compression-steps to get
rid of that LINCS warnings, and to have a stable system!
Is it maybe the prote
Edvin Erdtman wrote:
Hi
We have tried with no cutoff, as I have written in former emails, but
that was when we got trouble with LINCS warnings. We then thought that
we could try to continue remove lipids in the compression-steps to get
rid of that LINCS warnings, and to have a stable system
Try gromacs 3.1.4 make_hole version, downloadable from the user
contributions page. This works well for me. Alternatively, just select
a bunch of lipids to remove based on g_mindist and equilibrate -- 50ns
is cheap nowadays. The only reason that inflategro might be a huge
advantage is if yo
Greetings---
I'm working with a DNA system, and all of the routines I've worked with that
require Jacobi diagonalization (g_covar, g_rms, etc) fail with the "Too many
iterations in routine JACOBI" error. I'm using gromacs-3.3.3 with ffamber99
on the NCSA Mercury cluster. I've searched the archives,
> 1. A description of your system
I have a system of 250 5CB molecules (it is a liquid crystal) which means 4750
atoms.
> 2. Anything else that was printed to screen or the .log file (that's where
> the
> real error message will appear)
On the screen the message was
[compute-0-4:01361] ***
Antonia V. wrote:
> 1. A description of your system
I have a system of 250 5CB molecules (it is a liquid crystal) which
means 4750 atoms.
> 2. Anything else that was printed to screen or the .log file (that's
where the
> real error message will appear)
On the screen the message was
[c
I switched to v-rescale for the thermostat and things look normal!
Thanks for the help
Antonia
> Date: Wed, 1 Apr 2009 12:11:47 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] (no subject)
>
>
>
> Antonia V. wrote:
> > > 1. A description of your system
>
Hi Dayle,
Errm, really, the only cases I know of this error to occur is when I
had a mismatch between the reference and trajectory. Did you specify
xtc-groups? Did you shuffle the system? How did you assert that you
have matching series? Have you tried using the reference and the
trajectory to con
rlist 1.3 did the trick, thanks. Why did I not see this problem with
PME-switch?
Thanks,
Ilya
2009/4/1 Berk Hess
>
>
> > Date: Wed, 1 Apr 2009 14:15:05 +1100
> > From: mark.abra...@anu.edu.au
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] Energy Conservation with 4fs timestep
> >
Neha Gandhi wrote:
Dear List,
In the paper entitled "A new GROMOS force field for hexopyranose-based
carbohydrates" Journal of Computational Chemistry Volume 26 Issue 13,
Pages 1400 - 1412. When the authors ran unrestrained md for 2ns, once
the conformation is stabilised in chair, they donot o
Dear All,
I have been trying to determine why I am experiencing problems when I run
a gromacs file through x2top. I have checked my gromacs file with VMD to
ensure that the file is correct and VMD validates that my file is
correct as I see the intended structure. Thus, the atoms are indeed
located
darre...@ece.ubc.ca wrote:
Dear All,
I have been trying to determine why I am experiencing problems when I run
a gromacs file through x2top. I have checked my gromacs file with VMD to
ensure that the file is correct and VMD validates that my file is
correct as I see the intended structure. Thus,
Hi Tsjerk,
Thank you for your quick and helpful response. I defined "xtc_grps = TDR"
in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top
-o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with
-np 8.
I'm afraid that I don't understand what "shuffling" o
Dayle Smith wrote:
Hi Tsjerk,
Thank you for your quick and helpful response. I defined "xtc_grps =
TDR" in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p
topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL)
and run it with -np 8.
I'm afraid that I don't un
g_angle will do that fine, and with the options you used it should have done
so. Possible issue that may make that fail is you failed to generate the
correct angle index file for the dihedral(s) of interest.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Ph
Hi Mark
Sorry for the delayed reply. Somehow I missed your mail that time.
I am doing exactly what you have suggested. I am building up this missing part
and then trying to run the simulation.
Again 'm sorry for this delay.
Best regards,
Abhik
Abhik Mukhopadhyay
Departamento Química / Faculd
Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in
file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is the SOL
atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck
shows that the number of atoms in topol.tpr is 12284, but I still can't ge
Dayle Smith wrote:
Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms
in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is
Indeed, that's the problem, then!
the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and
now gmxcheck shows that t
Justin A. Lemkul wrote:
Dayle Smith wrote:
Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284
atoms in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The
difference is
Indeed, that's the problem, then!
the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and
Or rather than modifying the .top use tpbconv with an index file to
generate a new .tpr
Tom
--On Wednesday, April 01, 2009 21:15:34 -0400 "Justin A. Lemkul"
wrote:
Dayle Smith wrote:
Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms
in file") and gmxcheck -f traj.x
Thanks, Mark-
I re-ran a short MD simulation with TDR as the only xtc group, and used
tpbconv to create a .tpr file with only TDR (tpxout.tpr) and ran g_covar
with an index.ndx that contains only TPR (just to be safe!),
g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx
and I still get the Jacob
Hello,
I need some help figuring out how to compile gromacs on and sgi or linux
machine.
This is the error I get after using the make command to compile gromacs. Need
some suggestions. Thanks
source='gmx_wham.c' object='gmx_wham.lo' libtool=yes \
DEPDIR=.deps depmode=sgi /bin/sh
>Date: Wed, 01 Apr 2009 22:38:28 +0200
>From: David van der Spoel
>Subject: Re: [gmx-users] x2top & Encad all-atom force field (vacuum)
> not recognizing bonds
>To: Discussion list for GROMACS users
>Message-ID: <49d3d0c4.4040...@xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8
yimnai forlemu wrote:
Hello,
I need some help figuring out how to compile gromacs on and sgi or linux
machine.
This is the error I get after using the make command to compile gromacs.
Need some suggestions. Thanks
What compiler and compiler version are you using? It looks archaic, from
th
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