Oh thank you so much, I did not know it was a reference value. Given a
range of values might exist in one system I'm guessing minimization would
be the only way to deal with such a situation.
Best, Miro
On Sat, May 2, 2020 at 9:53 PM Justin Lemkul wrote:
>
>
> On 5/2/20 6:54 A
Hi all,
I'm trying to make a protein with a fair few disulfide bridges and I
couldn't get it to work. I chose -ss yes and increased the minimum distance
in specbonds.dat but it doesn't seem to want to let me see all possible
pariings.
Any way I can nudge it in the right direction without performi
Hi all,
I am interested in how Gromacs works at the back end but I don't have much
C experience so this might be silly.
I have noticed that one of my systems that includes virtual sites parses
fine through grompp in gromacs 2019.1 and 3 but fails in 2020.1 with a
segmentation fault.
21169 Segment
Incredible thank you.
On Wed., 15 Apr. 2020, 8:46 pm Justin Lemkul, wrote:
>
>
> On 4/14/20 10:12 PM, Miro Astore wrote:
> > Hello all,
> >
> > I am working with a rather large membrane bound protein. I was getting
> > an issue awhile ago where if the pro
Hello all,
I am working with a rather large membrane bound protein. I was getting
an issue awhile ago where if the protein moved to the edge of the box
the box would elongate in the z direction. I fixed this in the short
term by setting my xy compressibility to 0 in my production mdp file
pcoupl
90.548 3.5
-
Best, Miro
On Tue, Mar 31, 2020 at 9:58 AM Szilárd Páll wrote:
>
> On Sun, Mar 29, 2020 at 3:56 AM Miro Astore wrote:
>
> > Hi everybody. I've been experimenting with REMD for my system running
> > on
. I will soon see if i can get away with fewer replicas.
Thanks for your help. Miro
On Sun, Mar 29, 2020 at 9:04 PM Benson Muite wrote:
>
>
> On Sun, Mar 29, 2020, at 4:55 AM, Miro Astore wrote:
> > Hi everybody. I've been experimenting with REMD for my system running
> &g
correction: 99.3% is going into NxN
Ewald Elec. + LJ [F]
On Sun, Mar 29, 2020 at 12:55 PM Miro Astore wrote:
>
> Hi everybody. I've been experimenting with REMD for my system running
> on 48 cores with 4 gpus (I will need to scale up to 73 replicas
> because this is a compli
Hi everybody. I've been experimenting with REMD for my system running
on 48 cores with 4 gpus (I will need to scale up to 73 replicas
because this is a complicated system with many DOF I'm open to being
told this is all a silly idea).
My run configuration is
mpirun -np 4 --map-by numa gmx_mpi mdru
I have something like this on my github.
https://github.com/Miro-Astore/gromacs_scripts/tree/master/pbs_files/gadi
File is memb0.pbs let me know if you have any questions.
On Sat., 15 Feb. 2020, 8:45 am Neena Susan Eappen, <
neena.susaneap...@mail.utoronto.ca> wrote:
> Hello grom
Oh thank you very much I think I got confused looking at older documentation.
What sort of artefacts get created by using
comm-grps = Protein non-Protein?
On Wed, Feb 5, 2020 at 11:14 PM Justin Lemkul wrote:
>
>
>
> On 2/3/20 7:33 PM, Miro Astore wrote:
> > Hi everyone,
&g
Hi everyone,
I have tried using comm_grps to try and remove center of mass motion
from my system.
I used the following configuration
comm_grps = non-Protein Protein
nstcomm = 100
comm_mode = linear
comm_grps = non-Protein Protein
Would topotools in vmd not work in this context? I haven't used it but read
about it recently and it would seem this is the use case. Of course you
also need parameters. Wondering.
Best, Miro
Le sam. 1 févr. 2020 à 00:55, Justin Lemkul a écrit :
>
>
> On 1/31/20 8:25 AM, atb files wrote:
> >
>
Hello all,
I'm just wondering if gromacs supports constant x-y plane area for npt
simulations like NAMD does.
Best, Miro
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Hello all.
I need to use trjcat and trjconv often and I am wondering if there is any
way to speed up these utilities. They seem quite slow at the moment
compared to the catdcd binary in the vmd distribution.
Best, Miro
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Gromacs Users mailing list
* Please search the archive at
http://www.gro
Hi,
I'm new to gromacs myself. Your best bet if you're new to Molecular
dynamics is to do some tutorials and read best practices to try and
understand what the computer is actually doing and why.
http://www.mdtutorials.com/gmx/
I would recommend starting with the lysozyme in water tutorial as it
y and
secondary structures without the need for such a script, directly reading
itp files. Even being able to determine secondary structures from martini.
https://twitter.com/Matth_Chavent/status/1145727900286693376
Best, Miro
Le mer. 22 janv. 2020 à 20:07, Miro Astore a écrit :
> Does any
Does anyone know what the license is for the top2psf.pl script.
I'd like to modify and distribute it if possible.
Best, Miro.
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* Please search the archive at
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* Can't post? Read http://www.
t the most elegant way, but it works in my case.
> For more elegant ways, you could ask to VMD maillist.
> Best regards
> Alessandra
>
>
> On Tue, Jan 14, 2020 at 8:59 PM Miro Astore wrote:
>
> > Hi kenny, thanks for getting back to me.
> >
> > I use somethin
__
> Van: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> namens Miro Astore <
> miro.ast...@gmail.com>
> Verzonden: dinsdag 14 januari 2020 3:48
> Aan: gromacs.org_gmx-users@maillist.sys.kth.se <
> gromacs.org_gmx-
Hello all,
I'm just wondering how people load topologies for systems simulated in
gromacs into vmd. It is very annoying to have bonds that aren't in the
simulation placed in the visualisation. I'm wondering if anyone has a
solution that is easier than simply creating a psf file of the .gro system
Hello,
I am new to the gromacs work flow, I come from using NAMD.
An example of what I want to do is place harmonic restraints on a subset of
a molecule, for example all of the CA atoms in a protein backbone. I have
found the genrestr function which I would have expected would do the trick.
Howe
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