Hi
Thank you Mark.
On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham
wrote:
> Hi,
>
> Sorry I don't know how any of these non-GROMACS tools work, or even whether
> they actually generate Urey Bradley interactions that have all the terms. I
> suggest you spend some time with the documentation.
>
>
Hi,
Sorry I don't know how any of these non-GROMACS tools work, or even whether
they actually generate Urey Bradley interactions that have all the terms. I
suggest you spend some time with the documentation.
Mark
On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH wrote:
> Sorry Mark, I failed to note
Sorry Mark, I failed to note that.
I am afraid that I don't know what that are those components and how and
where to find it. If you are actually meaning about "ub0 kub" components,
how could i find the value for it. In case of swiss param generated itp
file, these components appear to be 0. Any
Hi,
Please read my answer.
Mark
On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH wrote:
> On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul wrote:
>
> >
> >
> > On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > > Dear all
> > >
> > > For grompp em.mdp I get an error
> > >
> > > ERROR 1 [file THC.itp, line
On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul wrote:
>
>
> On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > Dear all
> >
> > For grompp em.mdp I get an error
> >
> > ERROR 1 [file THC.itp, line 89]:
> >Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
> >
> > My itp file as foll
Hi,
The CHARMM software implements UB with two separate bond and angle
components, which you probably have to find and to insert here, to suit the
way GROMACS implements the interaction in a self-contained way.
Mark
On Wed, Dec 20, 2017, 10:36 AM Justin Lemkul wrote:
>
>
> On 12/19/17 11:14 AM
You can try rmsd and gyrate plot to see the changes in your complex. It
On Dec 19, 2017 2:22 PM, "RAHUL SURESH" wrote:
> Also you must know, a lot analysis are available over the entire manual of
> Gromacs where all cannot be performed. Gromacs always provide you all
> necessary analysis but to c
I used gmx mdmat in gromacs to create contact maps, but it seems that the
mdmat gives the minimum average distance rather than the average
centre-of-mass distance. Is there any way to get COM distance in gmx mdmat ?
--
Roshan Shrestha
M.Sc (Physics)
Central Department of Physics, Tribhuvan Univer
On 12/19/17 11:14 AM, RAHUL SURESH wrote:
Dear all
For grompp em.mdp I get an error
ERROR 1 [file THC.itp, line 89]:
Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
My itp file as follows
[ angles ]
1 2 29 579.178 109.588 *{Line 89}*
1 2 3 5
Dear GMX'ers, I'm wondering if you can give me some advice on setting up a
system containing a semipermeable membrane. I have seen a few comments on this
before, but I think my system is unique enough to warrant a new post.
I desire to run a system containing water, and many, largely anisotropi
Out of curiosity, how did you manage to identify and subsequently remove the
extra space? I have been having similar problems and the tools I've used
haven't fixed this problem.
Thanks,
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.o
Hello,
Im using g_membed to insert potassium channels into POPC membranes. My
"standard protocol" which worked very well for me on all proteins I used
so far seems to not work with gromacs 2018 (using the exact same input
files).
This is what I am doing:
1) orienting the protein onto the membra
- Message from Dhaniram Mahato -
Date: Tue, 19 Dec 2017 21:30:05 +0800
From: Dhaniram Mahato
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-us...@gromacs.org
Hi,
There could be format problem. You can create your own .dat files by
>>* I have a small problem with Gromacs, mainly with doing radius of gyration
*>>* calculations, it is all ok with doing the calcualtion, and the command is
*>>* fine but my problem is with the units in which the calculation is
*>>* performed. It is in picoseconds(ps) but i would like to have it in
which command line is used for SASA? i am using version 5.1.2
On Tue, Dec 19, 2017 at 9:53 PM, Mariia Savenko
wrote:
> Dear all,
> I have system in triclinic box. I'd like to plot a potential map on XY axes
> for a given Z in triclinic box, i.e. For a fixed value of Z I want to have
> plot of va
- Message from Dhaniram Mahato -
Date: Tue, 19 Dec 2017 21:30:05 +0800
From: Dhaniram Mahato
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-us...@gromacs.org
Hi,
There could be format problem. You can create your own .dat files by
Dear all,
I have system in triclinic box. I'd like to plot a potential map on XY axes
for a given Z in triclinic box, i.e. For a fixed value of Z I want to have
plot of values in this plane.
My system is a periodic "planar" molecule. Scripts using variations of the
Ewald summation are mainly intend
Dear all
For grompp em.mdp I get an error
ERROR 1 [file THC.itp, line 89]:
Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
My itp file as follows
[ angles ]
1 2 29 579.178 109.588 *{Line 89}*
1 2 3 532.192 112.817
2 3 31 551.424 10
Hi,
There could be format problem. You can create your own .dat files by typing
it. You have probably copied it from somewhere. I hope it will work then.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
Thanks
--
Gromacs Users mailing list
* Please search the
Hi all
I am doing umbrella sampling taking distance between COM as a reaction
coordinate. when I am trying to calculate PMF using the following command
gmx wham -it tpr-files.dat -if pullf-files.dat -o free.xvg -hist
hist.xvg
I got an error
Program: gmx wham, version 2016.3
Source file:
Hi,
An example where the structure comes from a single frame would be a useful
thing to explore whether the code is working correctly. I don't think the
composition of the index groups should matter, but I can't see how the code
wouldn't work correctly.
Mark
On Tue, Dec 19, 2017, 10:12 PM Anthon
Hi Mark,
As an example, from numerous attempts, I have tried:
/usr/local/gromacs5.1.2/bin/gmx_d distance -pbc -b 1 -f
crosslinked_0_20.trr -s crosslinked_0_20.tpr -n index.ndx
which was throwing a value of around 8 nm, rather than the 2 nm I was expecting
if it took a measurement from ove
Hi Alexandr,
Those were my thoughts also. I was just hoping there was something out there
already written to save me time.
Thanks
Anthony
Dr Anthony Nash
BSc (Hons) MSc MSc PhD MRSC
Department of Physiology, Anatomy & Genetics
Oxford University
OX1 3PT UK
On 19/12/2017 10:18, "gromacs.org_g
Hi
This is exactly what two well chosen selections should produce, given a tpr
and the PBC option. What have you tried that didn't work as you expected?
Mark
On Mon, Dec 18, 2017, 5:23 PM Anthony Nash
wrote:
>
> Hi all,
>
> I am trying to measure the distance between the COM of two side chain
Hi Anthony,
Would it work if you take x/y/z components of the distance and subtract
ones extending the size of the box in the corresponding direction?
You will need to extract box size from the *.edr file (unless box is of
fixed size), further use flag -oxyz from gmx distance for xyz distanc
Ok..Thank you..
I'll extend my simulation upto 50 ns.
Thanks,
Neha
On Tue, Dec 19, 2017 at 12:44 PM, Nikhil Maroli wrote:
> After MD simulation of protein-ligand complex for 5ns, can we view protein
> folding?
>
> mostly, NO
>
> Search what time range 'protein folding' is happening.
>
> How to
Hi Anthony,
I assume you've seen the -pbc flag of gmx distance; and IIRC there's
also some options for that in the selection syntax. I'm not sure that'll
do what you want though.
If you're going to make a script, have a look at the Python module
MDAnalysis, that has some nifty tools.
If you str
Also you must know, a lot analysis are available over the entire manual of
Gromacs where all cannot be performed. Gromacs always provide you all
necessary analysis but to choose which one is always your choice that suits
your simulation purpose.
On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta wrote:
On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta wrote:
> Hi,
>
>
> Thank you for your prompt reply.
>
> By clustering analysis, are you talking about gmx cluster command?
>
> "over particular PC sub space"
>
> Could you please elaborate a bit?
Yea clustering analysis can interpret a lot datas about
Hi,
Thank you for your prompt reply.
By clustering analysis, are you talking about gmx cluster command?
"over particular PC sub space"
Could you please elaborate a bit?
Thanks a lot once again.
Thanks,
Neha
On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH
wrote:
> On Tue, 19 Dec 2017 at 12:3
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