On 12/17/19 4:43 PM, D. Yousefi wrote:
I want to perform an MD simulation at high-temperature, and I need to
pre-equilibrate water molecules at that temperature before solvating my
protein so that the solvent reaches the correct density. What is the
appropriate way of doing this? As the first
On 12/18/19 6:40 AM, Quin K wrote:
I generated ligand topology using parachem website, I didn't do any
adjustments after, just used it as it is.
What do the penalty scores tell you about the quality of the parameters?
-Justin
On Tue, 17 Dec 2019, 1:11 pm Justin Lemkul, wrote:
On
Thanks for your information.
On Wed, 18 Dec 2019 at 12:30, Groenhof, Gerrit wrote:
> No, but this is possible in Charmm and in Amber.
> Best,
> Gerrit
>
>
>
> > Date: Wed, 18 Dec 2019 11:52:15 +0530
> > From: Muneeswaran S
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users] Constant pH
No, but this is possible in Charmm and in Amber.
Best,
Gerrit
> Date: Wed, 18 Dec 2019 11:52:15 +0530
> From: Muneeswaran S
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Constant pH replica exchange MD in Gromacs
> Message-ID:
>
> Content-Type: text/plain; charset="UTF-8"
>
> Good
Good Morning Friends,
I want to run Constant pH replica exchange MD
for my peptides. Is that possible with GROMACS?
please let me know. Its urgent.
--
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I generated ligand topology using parachem website, I didn't do any
adjustments after, just used it as it is.
On Tue, 17 Dec 2019, 1:11 pm Justin Lemkul, wrote:
>
>
> On 12/15/19 1:18 PM, Quin K wrote:
> > Hi
> > Thank you!!!
> >
> > Let's say during restraining of ligand, if I increased the
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=mdp#mdp-compressed-x-grps
And specify the particular atom in a group you pass in an index file to
grompp.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical
Hadi,
Anyway, you need the group of that single atom in your index.ndx file and
as you pointed out yourself the ``xtc-grps = single-atom'-group' flag will
do the job for you if you grompp -n index.ndx where the single-atom-group
presents in the index file.
Cheers,
Salman
On Tue, Dec 17, 2019 at
Hi Salman
Thanks, but in this way I will save trajectory of all of the atoms in the trr
file, and then I extract just the trajectory of my atom. However, what I need
is to avoid savimg lots of data. I needed an option in my mdp input file. Do
you have any idea for that?
Thanks
Hadi
Sent
Hi Haid,
In your index file, you should first generate a group which contains only
the atom of your interest:
gmx mak_ndx -f case.gro -o index.ndx
> a atom
> q
Then you can extract the trajectory of that single group (single atom)
using:
gmx trjconv -f traj.xtc -n index.ndx -o
Hello Dear gromacs users,
To reduce the size of my xtc file, I need to just extract the trajectory of
a especial atom, which is not an independent group, it is just one atom in
a group. I know that in md options I can narrow down trajectory of a group
(xtc_grps = XXX), but for just one atom or
I want to perform an MD simulation at high-temperature, and I need to
pre-equilibrate water molecules at that temperature before solvating my
protein so that the solvent reaches the correct density. What is the
appropriate way of doing this? As the first step, should I define my box
with water
Dear GMX users,
I have a question about enforced rotation. I would like to enhance rotation
around the peptide bond. Is it possible to rotate only the terminal amino acid
(or 2-3 AA) of an unfolded peptide? What kind of rotation should I use in that
case?
Harutyun Sahakyan
Senior Assistant
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