Hi,
The modified version of g_order provided as part of the SI in:
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00643#
should be able to calculate the order parameters radially from your protein.
Cheers
Tom
On 18 Mar 2020, at 11:02, Ipsita Basu wrote:
Dear all,
I want to calculate
I've not used this myself, but you can get them from:
http://vienna-ptm.univie.ac.at/?page_id=100
IIRC there are also conversion scripts on the GROMACS website too (in the user
contributions).
Cheers
Tom
On 24/06/2019 13:55, András Ferenc WACHA wrote:
Dear List,
I would like to use the
Hi,
Regarding g_order/gmx order being incorrect for unsaturated carbons, there is a
bug about this (https://redmine.gromacs.org/issues/1166). I would say that I
would fix it, but my C/C++ coding isn't good enough to be able to do this
properly. Perhaps a warning could/should be issued by the
If you are wanting to study things under physiological conditions I'd ask why
are you looking at DPPC?
Generally speaking physiological membranes are in the liquid crystal phase
(although this is a vast simplification of the heterogeneous and specialised
natures of different membranes) and
In the line you have added into the ffnonbonded.itp it looks like the numbers
for the LJ parameters have a comma rather than a point. So 2,47135e-01 rather
than 2.47135e-01. I imagine this is causing the too few parameters on line
warning
Cheers
Tom
= 1.4 more "adequate" than the
>> twin-range setup then ? Or is it just a "good to know" stuff ? I would
>> naturally use the fastest correct setup which seems to be the twin-range
>> one (with group-scheme), am I wrong ?
>>
> With the group cutoff scheme, simu
Hi,
In addition to Mark's comments, there are a few other points to be aware of:
1. If you use the twin-range scheme (i.e. 0.8/1.4) with nstlist 5, you need to
set nstcalclr to 1 to get results matching those as reported by Poger and
co-workers (see
Hi Peter/Emeliano,
I'm not sure I agree with some of what Peter says, but I guess it's probably a
matter of taste. If it were me, I'd definitely want my atomistic simulations to
behave properly before trying to develop CG parameters based upon these
simulations. I know that the coarse-graining
Yes, on Lipidbook. The force field is termed GROMOS-CKP. The parameters aren't
perfect but if you are wanting to go with a GROMOS united-atom force field,
these are AFAIK the best PG ones available.
Cheers
Tom
From:
I have some OPLS-AA ATP parameters that I made and tested ages ago, if you
really want them. But Justin is correct, there are almost certainly better
force fields to use with well validated ATP parameters and a better protein
force field than OPLS-AA/L (e.g. variants of the CHARMM and AMBER
Hi,
I don't believe this Chau paper is for deuterium order parameters (as I think
you are most likely referring to) but is related to some of the other order
parameter options in gmx order. The Vermeer paper you mention gives a good
overview of deuterium order parameters and you can find more
).
Cheers
Tom
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Piggot T.
[t.pig...@soton.ac.uk]
Sent: 09 February 2017 19:48
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Question
Hi,
Where did you obtain the POPG lipid topology from? From what I can remember,
this looks like the Elmore Berger based parameters. You need to have the
appropriate corresponding entries for all the itp atomtypes in your force field
files. That said, (if I've got the correct force field you
Hi,
I'd suggest it is a combination of 4 and 5.
It is still not completely clear how you are determining if the membrane is
classed as liquid disordered or not and also why you think it is too ordered in
your simulations at 350K (are they in a gel phase or just in a more ordered
state than
Hi Chris,
PG and PS have both been optimised for CHARMM36 (see
http://pubs.acs.org/doi/abs/10.1021/jp401512z), particularly in terms of
a reparameterisation of the lipid interactions with ions. That said,
from some recent work I have been doing with PS, it looks like (in
GROMACS at least)
You need to be a bit more specific. What other lipids do you have in the
membrane and which force field are you/do you want to use for these (and I mean
more than just GROMOS, but exactly which parameters they are e.g. 43A1-S3,
53A6L, etc.).
There are some GROMOS compatible force fields out
cified with -np/-nn or -conc, but I am likely to be wrong.
>
This is what the documentation says, and unless the code has been changed, I
recall finding that using -neutral on its own has no effect (would be a lovely
feature to have, though).
-Justin
> /J
>
> On Fri, Feb 19, 2016 at
tion says, and unless the code has been changed, I
recall finding that using -neutral on its own has no effect (would be a lovely
feature to have, though).
-Justin
> /J
>
> On Fri, Feb 19, 2016 at 12:18 PM, Piggot T. <t.pig...@soton.ac.uk> wrote:
>
>> Hi,
>>
>
Hi,
The -neutral option of genion should do the trick
Cheers
Tom
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of João Henriques
[joao.henriques.32...@gmail.com]
Sent: 19 February
Hi,
I have an itp for ATP that I made a while ago which has these parameters
included. I can send it off list if you like?
Cheers
Tom
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf
Hi Moritz,
For PG, issues with the Kukol parameters are briefly mentioned in the
Supporting Info of:
http://pubs.acs.org/doi/abs/10.1021/jp207013v
some of which (in particular the dihedrals around the double bond) are
discussed in more detail for POPC in:
Hi,
Neither of the two papers you mentioned use the Berger lipid parameters, rather
they both use purely GROMOS lipid force fields. This is plain GROMOS 45A3 for
the Chandrasekhar et al. paper (using older, original, GROMOS DPPC lipid
charges). This force field doesn't reproduce the properties
Hi Mohsen,
This table can indeed be quite confusing at first. I suggest you take a look at
http://redmine.gromacs.org/issues/773#note-10 where there is a discussion of
how to interpret table 8 (for a specific example, but it should highlight how
it works). Hopefully that should answer your
Hi Albert,
A simple script to run:
1) a short simulation
2) g_dist/gmx distance
3) g_analyze/gmx analyze
4) decide to continue the simulation from the final coordinates or restart the
simulation from the initial coordinates
should do the trick I think to reproduce the SuMD method given in
No, but you can download it from the user contributions part of the GROMACS
website:
http://www.gromacs.org/Downloads/User_contributions/Force_fields
Cheers
Tom
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
Hi Rebeca,
I would have thought you might be better, for an all-atom lipid force field, in
modifying the CHARMM force field based VMD tcl script. I believe g_order is
intended for united-atom lipids and so predicts the positions of the hydrogen
atoms based upon an idealised geometry. This
If you check out the second paper I linked to before ( the shameless plug to my
own work!), this should give you a good idea. That said, this work is a from a
few years ago now so there are some other parameters that are also now
available (google should find them for you).
Cheers
Tom
Hi Chris,
As far as I understand it, before GROMACS 5 the potential rather than the force
was switched off. Since GROMACS 5 you can choose between the two.
As for the settings to use with the CHARMM force field, the CHARMM package
itself (as Justin has said) uses force switching. However, in
...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul
[jalem...@vt.edu]
Sent: 19 May 2015 12:39
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs
version 4.6.7
On 5/19/15 5:37 AM, Piggot T. wrote:
Hi Chris,
As far
Hi,
In addition to my previous message, I thought i would also add in my 2 pennies
(cents) worth to the discussion on lipid force fields and cut-off's:
From the fairly large range of force fields and simulation parameters I have
looked at with simple PC membranes, Chris you are most definitely
Hi,
You can parse the output of -clid with a fairly simple script to obtain what
you need.
Cheers
Tom
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Steven Neumann
: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Piggot T.
[t.pig...@soton.ac.uk]
Sent: Wednesday, August 20, 2014 4:46 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated
residues
Hi
Hi Mike,
As well as the link that Bipin sent, you can also get parameters for GROMOS
phosphorylated residues (compatible with the 43A1 force field, I think) from:
http://www.gromacs.org/Downloads/User_contributions/Force_fields
I've never used either so have no idea which might be better. The
You can look at preview versions of some of the chapters from the GROMOS manual
on the ATB website:
http://compbio.biosci.uq.edu.au/atb/index.py?tab=forceField_tabnocache=752
Cheers
Tom
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
Hi,
You can have a look at:
http://pubs.acs.org/doi/abs/10.1021/ct3003157
In these simulations I used a few different variants in terms of both cut-off's
and the 'Berger' force field parameters, and so there isn't just one reference
value as the APL is dependent upon these different
Hi,
Here is a CG one:
http://lipidbook.bioch.ox.ac.uk/package/show/id/31.html
and here is an atomistic one:
http://lipidbook.bioch.ox.ac.uk/package/show/id/61.html
The atomistic one was used in a bacterial membrane, so you will likely have to
change the tails to make an appropriate
Hi David,
Firstly I would say, is there any reason why you need to use the
Berger/Höltje/GROMOS force field combination? There are several other options
available that I can think of which may be easier/better for you. You could use
the Slipids (with an AMBER force field for the protein),
Hi,
Personally I would also ask your colleague if he could also provide evidence
(e.g. published papers) to back up what he is saying to you (i.e. that it is
necessary to use a 1 fs timestep with an NVE ensemble to achieve acceptable
results). This way, you can make an informed decision based
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