GROMACS for this. I would like to run on a protein with oplsaa.
Is there someone here that successfully did a protein simulation in
GROMACS with implicit solvent and willing to explain the procedure and
share the parameters used (especially force field).
cheers,
Servaas
--
gmx-users mailing
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
kind regards,
Servaas
Message: 1
Date: Thu, 3 Dec 2009 11:23:14 +
From: Alan alanwil
servaas skrev:
Message: 4
Date: Tue, 1 Dec 2009 13:56:21 +
From: Alan alanwil...@gmail.com
Subject: [gmx-users] Re: amber force field in Gromacs
To: gmx-users@gromacs.org
Message-ID:
cf58c8d00912010556k5f2c918eqb2e1608c5c4cf...@mail.gmail.com
Content-Type: text/plain
Dear Servaas,
In tleap did you really did:
TLEAP
tleap -f leaprc.ff99SB
ad = sequence { DA5 DA DA3 }
saveamberparm da da_amber.top da_amber.crd
If so, it's wrong, it should be:
saveamberparm ad da_amber.top da_amber.crd
^^^
and not 'da'
Yes of course
-1; format=flowed
servaas wrote:
Hello,
I tried using the amber force field in GROMACS. I proceeded as follows:
Determined my parameters with RED/ANTECHAMBER/tleap converted them with
amb2gmx.pl
(or with acpypi, problem is the same) to gromacs coordinate and topology
files
. the one I found on the acpypi wiki.
servaas skrev:
Message: 6
Date: Tue, 01 Dec 2009 07:38:29 +1100
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] amber force field in Gromacs
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4b142d45.5050
Servaas,
I've been following your thread. I am the developer of acpypi and
thanks for giving a try.
So, as you may already know, you are trying acpypi as amb2gmx.pl so
far, but you also seemed to have read acpypi wikis and realise that
acpypi can help you to generate the whole topology
Hello,
I tried using the amber force field in GROMACS. I proceeded as follows:
Determined my parameters with RED/ANTECHAMBER/tleap converted them with
amb2gmx.pl
(or with acpypi, problem is the same) to gromacs coordinate and topology files.
It concerns a modified nucleotide. I minimized with
am prepared to help with it or test
it if this is required.
Kind regards,
Servaas
-
Message: 1
Date: Tue, 12 May 2009 09:06:52 +0200
From: Giovanni Bussi giovanni.bu...@gmail.com
Subject: [gmx-users] Re: v-rescale - harmonic oscillator
To: gmx-users@gromacs.org
Hi,
Thanks for your confirmation of this problem. One thing is not clear to
me from your answer. Has v-rescale fundamental problems with a Harmonic
oscillator or is it a problem with the GROMACS implementation?
Kind regards,
Servaas
Message: 3
Date: Fri, 8 May 2009 10:12:45 +0200
From
Article Number: 014101Published: JAN 7 2007 )
So what is going wrong here? Would one expect this thermostat to fail
for such system (e.g. a simple Nose-Hoover is known to fail for the
harmonic oscillator)?
Thanks in advance,
Servaas
___
gmx-users
Hi,
It is just a diatomic molecule without other interactions (so only
bonded interaction, LJ=0 and charges=0 on the atoms). What other details
would you like to know? Should I send you the tpr file?
Servaas
Hi,
No, only for small values is should be off, maybe tau_t 10 or 100
removing them with
comm_mode=angular be a problem then because you are using restraints?
(you use orire than?)
Thanks again,
Servaas
Hi,
With a diatomic molecule there is the issue that the rotation of the molecule
has two degrees of freedom
which are completely uncoupled from the rest
between odd replicas
and odd replica -1, when step/re-nst is even exchange is attempted
between even replica and even replica -1.
hope this helps,
servaas
On Tue, 2008-11-25 at 10:05 +0100, [EMAIL PROTECTED] wrote:
--
Message: 5
Date: 25 Nov 2008 09:05:35 -
From
The easiest is to use antechamber to generate your topology and then use
the amb2gmx.pl
(http://www.alchemistry.org/wiki/index.php/Image:Amb2gmx.gz)
To convert your amber topology to gromacs.
sevaas
Message: 2
Date: Sat, 18 Oct 2008 00:23:07 -0200
From: Ragnarok sdf [EMAIL PROTECTED]
In the [ defaults ] section change the combination rule.
servaas
Hi,
Is there a possibility when constructing the own .itp file to point
out Lennard-Jones (12, 6) parameters not in the form of C6 and C12 but
as sigma and epsilon.
Is there any key to switch this option?
Thanks
Or add option -all if you have several...
servaas
Message: 2
Date: Thu, 03 Jul 2008 10:36:56 +0200
From: Xavier Periole [EMAIL PROTECTED]
Subject: Re: [gmx-users] Dynamics : ONE dihedral angle time resolution
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: [EMAIL
For a given temperature, I will make them continues again then before
analysis.
Thanks for the help!
kind regards,
servaas
Hoi Servaas,
Was that the trajectory for a given temperature, or for a given
system? It should be for the latter, as otherwise, there will be weird
shifts introduced
Dear gromacs users,
I tried using trjcat like this:
trjcat -f gromacs*.trr -demux replica_index.xvg (see below for
replica_index.xvg and logfile)
there are 20 trajectories containing each 2001 frames, with timestep of
0.5ps (I checked it with gmxcheck).
The error:
Reading frame 60
the problem, this makes that there are jumps in the trajectory of
course...
kind regards,
servaas
servaas michielssens wrote:
Dear gromacs users,
I have a problem that is already discussed a lot on the mailing list,
in a protein-ligand simulation the ligad jumps out of the box
If you have amber, you can make your topology in amber and convert them to
gromacs with the script on this website:
http://chemistry.csulb.edu/ffamber/tools.html
kind regards,
servaas
Dear all,
Sometimes,the PDB file contains water molecules which only have the
oxygen atom. Can
). But
this did not help.
What I am doing wrong here?
thanks in advance for your help!
kind regards,
servaas
___
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http
chemical chemical calculation or use equivalent
parameters. (but this is more a topic for the amber mailing list...)
kind regards,
servaas
Message: 6
Date: Mon, 31 Mar 2008 10:25:17 -0400
From: Xiangyu Fan [EMAIL PROTECTED]
Subject: Re: [gmx-users] Re: Help needed on using general amber force
/ffamber/
kind regards,
servaas
Date: Thu, 13 Mar 2008 22:57:29 -0400
From: Xiangyu Fan [EMAIL PROTECTED]
Subject: [gmx-users] Help needed on using general amber force field
(GAFF) in Gromacs
To: gmx-users@gromacs.org
Message-ID:
[EMAIL PROTECTED]
Content-Type: text/plain; charset
I ran the following command in gromacs:
editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8
The equivalent command in amber:
solvateoct p61_vac.pdb TIP3PBOX 8.0
As far as I understand this, both command created a box were the edges are 0.8
nm away from the solute. But the
[EMAIL PROTECTED]
Subject: Re: [gmx-users] parallel simulation crash on 6 processors
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
servaas michielssens wrote:
I tried to run a gromacs
there was no problem.
kind regards,
servaas michielssens___
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Please don't post (un)subscribe
Date: Wed, 21 Nov 2007 14:03:53 -0800
From: David Mobley [EMAIL PROTECTED]
Subject: Re: [gmx-users] restart an amber run in gromacs
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
[EMAIL PROTECTED]
Content-Type: text/plain; charset=ISO-8859-1
Hi,
servaas michielssens
that amber
could simulate 1.5ns/day and gromacs only 1ns/day. This was a surprise
to me, I expected that gromacs would be faster. Could it be that using
gromacs with the amberFF is not faster than just using amber? I am new
to gromacs and perhaps I didn't compare them correct.
kind regards,
servaas
to run it after minimalization and this worked fine. So there
seems to be a problem while converting the files, I am new to gromacs
and I don't really have a clue how to find the cause of this problem,
perhaps some of you also tried to continue a amber run in gromacs?
kind regards,
servaas
to run it after minimalization and this worked fine. So there
seems to be a problem while converting the files, I am new to gromacs
and I don't really have a clue how to find the cause of this problem,
perhaps some of you also tried to continue a amber run in gromacs?
kind regards,
servaas
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