Dear gromacs users
In a recent paper I found the following protocol of a gromacs simulation:
"All simulations were performed with the GROMACS 4.0 [12] compiled in single-precision mode at a constant temperature of 277 K in a periodic box with an edge length of approximately 8.2 nm and the defaul
Am 04.04.2012 14:03, schrieb gmx-users-requ...@gromacs.org:
Bernhard Knapp wrote:
> Hi
>
> I have some problems to get do_dssp running:
>
> I downloaded the binary of dssp fromhttp://swift.cmbi.ru.nl/gv/dssp/ .
> Then I extracted it using "gunzip dssp-2-linux-
Hi
I have some problems to get do_dssp running:
I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using
"gunzip dssp-2-linux-i386.gz". Next I copied it to the correct location: "cp
dssp-2-linux-i386 /usr/local/bin/dssp" and gave the user the right to e
Dear users
Due to a hard disk crash we lost several md simulations. Fortunalty we
have backup copies of the trajectry files (xtc format) and structure
files of the first frame of the simulation (created via trjconv -b 0 -e
0 -f myName.md.trr -o myName.md.firstframe.pdb -s myName.md.tpr). We
The whole complex consists of 5 chains (MHC-alpha, MHC-beta, epitope,
T-cell receptor alpa, T-cell receptor beta).
What you can see in
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg
is exactly the same angle. The two
1) trjconv with the "-pbc nojump" option does not help - it removes most
of the jumps but one big remains- the rmsd for the trajectory is
http://www.meduniwien.ac.at/msi/biosim/bk/4.jpg
before the converting with -pbc and
http://www.meduniwien.ac.at/msi/biosim/bk/4noJump.jpg
after conversion.
in
Dear users
I performed some long-time simulations using gromacs 4.0. The longest
simulation trajectory is about 62 ns. Unfortunately the trajectory seems
to be damaged. If I calculate the RMSD of different interesting regions
the values are beginning to jump up an down after about 17 ns in one
Dear users
Are there any hardware preferences for using Gromacs with best
performance? The ones from the Gromacs FAQ seem quite out dated to me.
So which hardware infrastructure would you buy with 35k euro?
cheers
Bernhard
___
gmx-users mailing list
Hi
I installed Gromacs successfully on Fedora 8 nodes. Afterwards I ran a
successful small simulation. Thereafter I moved the node to our
server-room did the following:
- set ip adress, subnetmask and gateway
- changed the ssh port in /etc/ssh/sshd_config since we use port
forwarding on our r
If someone is interested: Finally our nodes are working fine using
Fedora Core 8, fftw-3.1.3, openmpi-1.3 and gromacs-4.0.3. Thank you very
much for your time and effort!
cheers
Bernhard
Message: 2
Date: Thu, 15 Jan 2009 08:37:16 +0100
From: patrick fuchs
Subject: Re: Subject: Re: Re: [gmx
Hi Berk,
I continued the simulation and it works fine (for the next few hours).
Then it gets stuck again. So it seems that the problem is not directly
related to gromacs. But it seems the interaction between the operating
system or the hardware does not work for a longer time.
We are using ope
Mark wrote:
What's happening in the log files? What's the latest information in the
checkpoint files? Could there be some issue with file system availability?
Hi Mark
Unfortunaltey I already deleted the simulation files which got stuck
after 847ps. But here is the output of another simulatio
Dear users
I have a problem with gromacs 4 (also tried 4.0.2). If I start a
simulation it is calculating for some time but after about one day it
gets somehow stuck. This means that the simulation is still running and
the top commands says md still uses all 4 cores of the computer:
5487 bkna
> Justin wrote:
It looks like your coordinate file is from
PRODRG; why not use PRODRG to generate a rough topology, and refine it according
to the ffG43a1 parameters?
The problem is that the sugar in in contact with a bigger protein complex and
the PRODRG server is not willing to accept mo
Dear Users
I tried to use the x2top function of gromacs 4 on a sugar-molecule. But
the gromacs says that it requests the ffgmx.n2t library which can not be
found in the default directory. I searched in the whole system but could
not find it. Therefore I also searched on an other system with gr
Dear users
I am trying to minimize the energy of a complex using gromacs 4. The
commands are the following:
pdb2gmx -f full_mCARKL_to_xylose_kinaseFH.pdb -o
full_mCARKL_to_xylose_kinaseFH.gro.pdb -p
full_mCARKL_to_xylose_kinaseFH.top -ignh
editconf -f full_mCARKL_to_xylose_kinaseFH.gro.pdb -
o check out the documentation resources and manual, e.g.
http://wiki.gromacs.org/index.php/FAQs
x2top and the prodgr web-server might be some good starting points.
Andreas
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Knapp
Sent: 19 November 2008 12:54
To: gmx-users@gromacs.or
Dear users
I would like to perform a MD simulation of Sedoheptulose (C7H14O7) via
Gromacs. But already during pdb2gmx it comes up with:
"Residue 'UNK' not found in residue topology database" which is
obviously clear since sedoheptulose is not an amino acid. Is it somehow
possible to simulate t
hi
is there any new information on the release of gromacs 4? currently we
are planning to install gromacs on a new cluster and we are not sure if
it is worth to install the old 3.3 version or to wait for the 4.0 release?
thx
Bernhard
--
Bernhard Knapp
Unit for Medical Statistics and
Hi there,
I wanted to ask if gromacs is able to deal correctly with peptides which
have been acetylized at the N-terminal end? if so what would be the
approbriate way (tool) to model the acetyl?
thx
Bernhard
--
Bernhard Knapp
Unit for Medical Statistics and Informatics - Section for
20 matches
Mail list logo
