Hi,
Is there any possible way where I can get the ClayFF force field directory
files for koalinite for GROMACS?
Thank you in advance.
*NURUL HAYATI BINTI HAROLANUAR*
Bachelor of Engineering (Hons) Petroleum Engineering
Universiti Teknologi PETRONAS
32610 Bandar Seri Iskandar,
Perak Darul
First off, you should keep this on the emailing list. I have included the
emailing list in the reply. No need to take it to private email.
Did you read the link that I sent with the reply? You even have the
simulation box visualised with the vmd screen shot you sent, so that should
be a big
Dear all,
I'm currently trying to locate the latest version of acpype and have been
unable to find a working link to the script/installer. Could anyone please
point me in the right direction?
Thanks,
Matthew Fisher
--
Gromacs Users mailing list
* Please search the archive at
Dear Justin,
I'll take a look at the comments.
Thanks for the quick reply.
Best,
Carlos
El mar., 23 oct. 2018 a las 15:17, Justin Lemkul ()
escribió:
>
>
> On 10/23/18 2:15 PM, Carlos Navarro wrote:
> > Dear gromacs users,
> > Where can I download the charmm36m version of charmm for gromacs?
> >
On 10/23/18 2:15 PM, Carlos Navarro wrote:
Dear gromacs users,
Where can I download the charmm36m version of charmm for gromacs?
I know that here :http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs is
It's CHARMM36m. See the comments at that link that explicitly say what
is included
Dear gromacs users,
Where can I download the charmm36m version of charmm for gromacs?
I know that here :http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs is
the charmm36 version, but since I'm preparing some parts in charmm-gui, I
want to try the charmm36m version instead.
Hope someone can
Dear all,
I would like to obtain a 2D density map plot as for instance Fig. 4 in the
following paper (DOI 10.1007/s00232-014-9690-8) for a membrane protein inserted
in a surfactant micelle with gmx densmap and xpm2ps . I have few questions
- Have any of you ever done this type of plot? If
Dear GMX users,
I would like to share a difficulty installing GROMACS/2018.3 with you. I
use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU nodes
equipped with 4 x P100 Nvidia devices.
Below is the cmake configuration that I use, followed by the error that I
receive. I am not sure
On 23.10.2018 15:12, Michael Brunsteiner wrote:
> the computers are NOT overclocked, cooling works, cpu temperatures are well
> below max.
> as stated above something like this happened three times, each time with gmx
> at full blastand with the same type of nvidia card ... can it be that my
>
BS”D
I had a similar issue with a workstation, and it turned out to be the power
supply, which is why it seemed that someone pulled the plug (at least it seems
to be the PSU, since having replaced it we don’t see failures). The problem
was very intermittent, and did not require any great
Hi,
this might be considered off-topic, but i believe there is some evidence to the
contrary ... what i see is this:
I have a couple of (fairly new) workstations (specs below) and on at least two
of them, on at least three differentoccasions, i recently saw the following
behaviour:computer is
On 10/23/18 8:08 AM, Quyen Vu Van wrote:
Dear Justin,
Thanks for your respond.
What if I mean turn off residues just by remove the non-bonded term and
then gradually adding non-bonded interactions back?
I understand exactly what you're trying to do and my comments are a
direct response to
Dear Justin,
Thanks for your respond.
What if I mean turn off residues just by remove the non-bonded term and
then gradually adding non-bonded interactions back?
Best regards,
Quyen
On Mon, Oct 22, 2018, 14:11 Justin Lemkul wrote:
>
>
> On 10/22/18 7:29 AM, Quyen Vu Van wrote:
> > Dear all,
> >
Hi,
Following may be helpful:
http://manual.gromacs.org/documentation/2019-beta1/user-guide/force-fields.html#gmx-amber-ff
Regards,
Benson
On 10/23/18 11:52 AM, farial tavakoli wrote:
> Dear GMX users
> I need to simulate the complex composed of a protein and a peptide which has
>
Dear GMX users
I need to simulate the complex composed of a protein and a peptide which has
phosphotyrosine using AMBER99SB force field in GROMACS. cited to the "
https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/index.html "
to download .OFF and .FRCMOD files of phosphotyrosine.
Yes thank you I thought it had to be specified with a specific command in
GROMACS.
In effect, just linux works.
Francisco
On Tue, Oct 23, 2018 at 10:15 AM Peter Stern
wrote:
> Hi,
>
> This is really a linux and not a gromacs question. There are many ways of
> inputting data to a script
Thank you, that worked.
Francisco
On Tue, Oct 23, 2018 at 10:14 AM Mark Abraham
wrote:
> Hi,
>
> See http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> Mark
>
> On Tue, Oct 23, 2018, 09:28 Francisco Lobo Cabrera <
> francisco.lo...@gmail.com> wrote:
>
> > Hello:
> >
> >
Hi,
This is really a linux and not a gromacs question. There are many ways of
inputting data to a script depending upon which shell you use.
One way is to input the data from a file.
You should google how to do this for the shell you use (bash, tcsh, etc.) and
choose the solution which suits
Hi,
See http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
Mark
On Tue, Oct 23, 2018, 09:28 Francisco Lobo Cabrera <
francisco.lo...@gmail.com> wrote:
> Hello:
>
> Is it possible to specify several index groups through the command line?
>
> For example, to compute hydrogen
Hello:
Is it possible to specify several index groups through the command line?
For example, to compute hydrogen bonds, hbond needs two index groups. This
can be done through the interactive prompt, but I need to submit this
instruction wtih a script. I have searched around but have not found
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