Hi all,
I am working on the Hydration dynamics studies on Aquaporin 0 which is
membrane protein, Downloaded from the MemProt database and performed
production MD for a time scale of 100ns. I am facing difficulty in
identifying and eliminating the time period for which the system has
undergone equ
Dear Prof. Dan,
Thank you very much for the suggestion. However, when I gave the command;
gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx in
VMD TkConsole, I didn't get any output.
I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90
and y. What could b
Never dealt with TiO2, but the path to parameterizing forcefields for
solid-state structures in MD is becoming more and more straightforward,
e.g., J. Phys. Chem. C 2017. 121(16): p. 9022-9031.
Alex
On Thu, Sep 27, 2018 at 4:11 PM paul buscemi wrote:
> Alex,
>
> There are so many important rea
figured it out ... hwloc version 2.0.2 was too new ... oncei used hwloc-1.11.11
instead things worked ...
mic
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Alex,
There are so many important reactions / applications in which protein polymer
interactions play a role that the ability to generate of polymers should be
part of gromacs repertoire. I’ll keep plugging away on this and report to the
community if I can break the code - other than using
antonio.gromacs.carle...@gmail.com
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Hi all,
I would like to take the distance over time between two pair of atoms.
I used gmx distance.
to check the value I download the snapshot every 100 ns..
When the distance is within the unit cell everything should be fine.
when the distance increase the value seems not to be correct ( comp
Hi,
In the past I compiled gmx 2016.4 on our old cluster and this worked as
expected.
Now I just compiled 2018.3 only to find that the resulting binary was
unexpectedly slow ...
On each node I have a multi-core architecture with 12 logical threads,
but htop shows that gmx uses only one thread.
Hi Paul,
Glad x2top is working out for you. The rest of the things you're
pointing out, I hope others could comment. I haven't simulated any
proteins in a long time, but if you ever need to drop a protein on the
surface of some sort of an insane molybdenum disulfide-graphene-boron
nitride het
Hi,
I have functionalized Mn-cdS nanotube by amino acid,... . New O-S bond,
Mn-O bond,... formed. Now i want to do MD simulation for this
functionalized nanotube. (I use AMBER99SB ff)
How should i define ffbonded.itp?I have bond length and angles but i don't
know kb. If for example kb of Mn-O for
Hi,
The default behaviour is to consider atom positions, but you want to
include atoms based on e.g. molecule position. IIRC use -selrpos mol_cog
for that (or similar changes within the selection). See the final examples
at
http://manual.gromacs.org/documentation/2018/onlinehelp/selections.html#se
Thanks Mark.
The gmx select and then gmx trjconv work fine and I have a box with a more
or less desirable region being solvated by water.
However there is only one problem and that is the SOL's molecules in the
border of the region ( resname SOL and z>= 2 ). By that the Water molecules
in the borde
Alex,
This pertains the prior correspondence to building a polymer and is the process
I've been developing.
To date I can obtain an ITP and pdb from ATB for a monomer. From there with
information in those files, it is relatively easy to construct the n2t file to
use in x2top. ( I’d be happ
Hi,
No, but you can use gmx select to make such a selection from the
fully-solvated box, and gmx editconf (maybe) or gmx trjconv (definitely) to
end up with the content you want. (We'd like to make this functionality
more generally available, but it's not ready yet...)
Mark
On Thu, Sep 27, 2018
Dear all,
I wonder if it is possible to solvate just a part of a box using gmx
solvate. For example suppose you have a box with the lengths of x, y, z,
then, how I can solvate only a part of it like (x, y, z with z> 2)?
Thanks
Alex
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ht
Doesn't gmx sigeps do what you need?
Dan
On Wed, Sep 26, 2018 at 10:44 AM Sam David wrote:
> What is your system?
> Try to do a fitting and check. I have the same problem and still trying
>
> Good luck
> Sam
>
> On Wed, Sep 26, 2018 at 9:08 AM sanjeet kumar singh ch16d012 <
> ch16d...@smail.iit
Hi,
I believe you are trying to select atoms/particles that are in an
infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and
(90, 125)?
Gmx select uses commands that are similar in syntax to a software called
VMD. So I like to use VMD to figure out what I need to give to gmx sele
Thank you so much for your information.its really help me a lot.
On Sep 27, 2018 3:07 PM, "Peter Kroon" wrote:
> No, this is not correct.
>
> Prehaps I worded my first e-mail too subtly. The secondary structure of
> a protein in a normal Martini simulation *will not* change. Trying all
> sorts o
Dear Gromacs users,
I want to make an index files with molecules in a particular area. I have
four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which
define an area of the system. How can I do it with gmx_select?
Can anyone help me?
Thank you.
On Thu, Sep 27, 2018 at 4:14 PM Sh
Hi Mark,
Thanks. If the answer to q. 1 is no, then I will just stick with something
like 3-4 digits.
Alex
On Thu, Sep 27, 2018, 3:56 AM Mark Abraham wrote:
> Hi,
>
> 1. No. 2. From the look of
>
> https://github.com/gromacs/gromacs/blob/master/src/gromacs/gmxpreprocess/nm2type.cpp#L91
> ,
> yo
Hi,
1. No. 2. From the look of
https://github.com/gromacs/gromacs/blob/master/src/gromacs/gmxpreprocess/nm2type.cpp#L91,
you could supply as many as fits in a double-precision value (maybe about
15), but whether the subsequent calculations retain the precision is
unclear without a detailed look at
Hm, i thought it was a question someone could answer...
On Sat, Sep 22, 2018, 10:52 PM Alex wrote:
> Hi all,
>
> I am dealing with a solid structure with partial charges initially
> obtained from DFT and adjusted to work with MD. It just so happens that
> the total charge of the system, however
No, this is not correct.
Prehaps I worded my first e-mail too subtly. The secondary structure of
a protein in a normal Martini simulation *will not* change. Trying all
sorts of tricks to make the analysis program happy will not change this.
The secondary structure is fixed by your topology. Either
Hi,
On Thu, Sep 27, 2018 at 12:45 AM Mario Andres Rodriguez Pineda <
mand...@iq.usp.br> wrote:
> Hi again every body.
> I'm tryin running a simulation of a protein in water using Gromacs 2018.3.
> When i try to minimize the energy in NVT equilibration this send me this
> error during mdrun:
>
> R
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