Hi,
The name of the residue in that force fields aminoacids.rtp is CLA, which
is the only thing pdb2gmx can understand. Otherwise your procedure should
just work if you rename your ion residues appropriately. Do let us know how
you go!
Mark
On Wed, Jul 18, 2018, 03:23 Anderson, Amos wrote:
> H
Dear Justin,
I have tried the same commands with gromacs version 5.1.2 and the same
errors arise.
You have suggested that the format of what has been provided to grompp may
be wrong. What I did was modify ffnonbonded.itp by leaving the C6, C12
columns empty alongside pair interactions under the [no
On 7/17/18 9:22 PM, Anderson, Amos wrote:
Hi Gromacs users,
I’ve never used gromacs before, so sorry if this question has an obvious answer
somewhere — it seems like the sort I should have been able to find an answer
for…
I want to write a python script to prepare an arbitrary pdb for use
Hi Gromacs users,
I’ve never used gromacs before, so sorry if this question has an obvious answer
somewhere — it seems like the sort I should have been able to find an answer
for…
I want to write a python script to prepare an arbitrary pdb for use with
gromacs (e.g., does these steps
http://w
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
On Tue, 17 Jul. 2018, 11:12 pm neelam wafa, wrote:
> Hi,
>
> Dear gromacs users, I am running md simmulation of a protein with a ligand.
Monitor your property of interest, then when it has reached a stable value
for a length of time (need to consider how long takes to stabilise to how
long that should be), then you can start to think it may be at
"equilibrium". Depending on the property of interest though, you have to
chance if ran
-- Forwarded message --
From: neelam wafa
Date: Tue, Jul 17, 2018 at 1:12 PM
Subject: problem in energy minimization
To: gromacs.org_gmx-users@maillist.sys.kth.se
Hi,
Dear gromacs users, I am running md simmulation of a protein with a ligand.
i have already done it with the same
Hello,
In the OPLSAA ffbonded.itp, it is also mentioned that improper torsions for
planar groups are implemented in gromacs as proper dihedrals. So, I think
you are using the wrong function type here (type 2); you should use type 1
in this case.
Hope this helps.
Best,
Abhishek
On Tue, Jul 17,
Hi Justin,
Thank you for getting back to me. After estimating the resulting reduction in
system size, in this case I decided to live with the extra water molecules.
However, it’s good to know that any system adjusted this way requires both
minimization and equilibration.
Best,
Roman
> On Jul
Dear all,
How to understand whether a system(large system) reaches equilibrium after
MD simulation?
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Hello all,
I'd like to simulate a Lennard-Jones mixture.
For simplicity, let's say it's a binary A B mixture.
However, sigma_AB and epsilon_AB are set independently (i.e. NOT derived from a
standard mixing rule of AA and BB parameters).
In addition, I'd like AA, BB, and AB interactions to all ha
Hi,
Dear gromacs users, I am running md simmulation of a protein with a ligand.
i have already done it with the same protein and a different ligand. Now
when i run em md run i get following result.
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax
one more question about the pull code.
I have outputted the force for pulling the molecule in .xvg file. If I pulled
the molecule in Z direction, does the positive sign in front of the force mean
the direction of the pulling force is identical to the positive direction of
the Z axis?
Fan
Hi,
Generally there is useful information in the header of the .xvg file, which
people might be able to help interpret. They will also want to know what
command you ran, and from what version of GROMACS, because these things can
vary over time.
Mark
On Tue, Jul 17, 2018 at 2:37 PM SHYANTANI MAIT
Thanks Justin
Fan
-- Original --
From: "Justin Lemkul";;
Date: Jul 17, 2018
To: "gmx-users";
Subject: Re: [gmx-users] what is the force on the energy group when pullcode
is used?
On 7/17/18 6:03 AM, 1185201182 wrote:
> Dear users
>
>
> I am using
Dear all,
What should be the format of xvg file for calculating the time correlation
function in gromacs?
I am using this format(1st and 3rd column are the time steps)
0 -1.73312 0 5.43112
2 -0.84264 2 8.65560
4 -0.89785 4 2.14901
6 1.613256 2.87340
8 -2.32500 8 0.48249
10 1.82224 10
On 7/17/18 6:03 AM, 1185201182 wrote:
Dear users
I am using the pull code to pull one of molecules in my simulation and the
molecule which is pulled is also defined as an energy group in my mdp file,
then I output the force in trr file
So I wonder if the force on the pulled molecule i
On 7/17/18 5:40 AM, Apramita Chand wrote:
Dear All,
I had enquired earlier about the steps for changing combination rules in
GROMOS ff. As I understood from your answers, if I am to take combination
rule 3, I can put sigma and epsilon for my atomtypes under the C6 and C12
columns in ffnonbond
On 7/17/18 3:10 AM, atb files wrote:
Dear experts,How can I find the tilt in the lipids of the Bilayer with respect to Bilayer normalAny gromacs tool which can do this.ThanksYogiSent using Zoho Mail
gmx bundle and gmx gangle can both do this.
Justin,
Lovely advice. I'll definitely consider it :) Thank you.
Regards,
Rajat
On Mon, Jul 16, 2018 at 11:15 PM Justin Lemkul wrote:
>
>
> On 7/16/18 1:42 PM, Rajat Desikan wrote:
> > Hi Mark,
> >
> > Thank you for the quick answer. My group is experimenting with a
> GPU-heavy
> > processor-l
Dear users
I am using the pull code to pull one of molecules in my simulation and the
molecule which is pulled is also defined as an energy group in my mdp file,
then I output the force in trr file
So I wonder if the force on the pulled molecule in the trr file just includes
the force fro
Dear All,
I had enquired earlier about the steps for changing combination rules in
GROMOS ff. As I understood from your answers, if I am to take combination
rule 3, I can put sigma and epsilon for my atomtypes under the C6 and C12
columns in ffnonbonded.itp and these numbers will be interpreted a
Dear experts,How can I find the tilt in the lipids of the Bilayer
with respect to Bilayer normalAny gromacs tool which can do this.ThanksYogiSent
using Zoho Mail
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* Please s
Hi,
That depends what your other inputs are. See the reference manual, chapter
2.
Mark
On Tue, Jul 17, 2018 at 5:05 AM Brandon Wiebe wrote:
> Thank you, Justin.
>
> So if I wanted to simulate a system of Lennard-Jones particles under the
> NPT ensemble using reduced units, would I need to set
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