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 +
> F
> 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
> servaas skrev:
> >> Message: 4
> >> Date: Tue, 1 Dec 2009 13:56:21 +
> >> From: Alan
> >> Subject: [gmx-users] Re: amber force field in Gromacs
> >> To: gmx-users@gromacs.org
> >> Message-ID:
> >>
> >> Con
> Message: 4
> Date: Tue, 1 Dec 2009 13:56:21 +
> From: Alan
> Subject: [gmx-users] Re: amber force field in Gromacs
> To: gmx-users@gromacs.org
> Message-ID:
>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Servaas,
>
> I've been fol
tried
different settings, e.g. the one I found on the acpypi wiki.
>
> servaas skrev:
> >> Message: 6
> >> Date: Tue, 01 Dec 2009 07:38:29 +1100
> >> From: Mark Abraham
> >> Subject: Re: [gmx-users] amber force field in Gromacs
> >> To: Discus
>
> Message: 6
> Date: Tue, 01 Dec 2009 07:38:29 +1100
> From: Mark Abraham
> Subject: Re: [gmx-users] amber force field in Gromacs
> To: Discussion list for GROMACS users
> Message-ID: <4b142d45.5050...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859
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 s
is. I 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
> Subject: [gmx-users] Re: v-rescale - harmonic oscillator
> To: gmx-user
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
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 uncouple
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 ta
conserved for this system. (of course there can also be an error in my
hybrid monte carlo code, but the fact that the conserved energy is not
conserved is disturbing me here)
Servaas
Hi,
What do you mean with effective energy?
The Gromacs conserved energy term?
For very small tau_t the current
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
exchange is attempted 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:
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]>
>
, you could consider using RESP charges. Did
you compare your parameters do published pyrophosphate parameters e.g.
http://www.pharmacy.manchester.ac.uk/bryce/amber
hope this helps,
servaas
> Dear people,
>
> I have parameterized a ligand with one phosphate and one pyrophosp
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
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
Message-ID: <[EMAIL
What box type are you using? Try adding following options
-center -pbc mol -ur compact
kind regards,
servaas
Hi all,
During my MD the molecule experience a drift. Now I want to put the
molecule at the center of the water box.
I tried with trjconv using the -pbc mol and -center flag and
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 time
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
auses 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
this did not help.
What I am doing wrong here?
thanks in advance for your help!
kind regards,
servaas
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http
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
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 gen
b.edu/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]&g
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 resu
I made a mistake in the numbers, but the question remains:
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 w
+0100
> From: David van der Spoel <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] parallel simulation crash on 6 processors
> To: Discussion list for GROMACS users
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
&
problem.
kind regards,
servaas michielssens___
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Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subs
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"
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
Message: 1
Date: Wed, 21 Nov 2007 21:54:57 +0100
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] gromacs preformance versus amber
To: Discussion list for GROMACS users
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flo
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,
se
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,
se
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,
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