Hello Dear Gromacs users,
I hope this email finds you well. I am sending this email to ask is there
any way I can convert gromacs topology file (.itp) to namd (top) file? I
appreciate any help,
Best regards,
Hadi
--
Gromacs Users mailing list
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Hello Gromacs users,
I hope you are well. I am doing a simulation to get the diffusion
coefficient of some gas molecules in a material structure. After
minimization and solvation, I run NVT and then NPT to equilibrate the
system, and then for production again I am running NPT step. My first
> Then you can extract the trajectory of that single group (single atom)
> using:
>
> gmx trjconv -f traj.xtc -n index.ndx -o atom.xtc
>> choose the group of your interest here!
>
> Regards,
> Salman
>
> On Tue, Dec 17, 2019 at 4:04 PM Hadi Rahmaninejad
> wrote:
>
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
>
> >
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Hadi
> Rahmaninejad
> > Sent: Thursday, November 7, 2019 10:04:58 AM
> > To: gmx-us...@gromacs.org
Hello gromacs users,
Can any body give me a reference page in gromacs manual for printing option
in energy minimization? I know for nvt other steps, but in energy
minimization it automatically prints a lot of "stepXXX.pdb" which are
unnecessary and I want to avoid that.
Thanks,
Hadi
--
Gromacs
you want
> to
> > do the same operation for multiple files, I would suggest checking out
> bash
> > programming for doing that.
> > I hope this will help you.
> >
> > Chenyu Liu
> >
> > On Tue, Oct 1, 2019 at 3:46 PM Hadi Rahmaninejad
> > wrote:
Hello Gromacs Users,
I am going to use "trjconv" to extract trajectory from a .trr file. Here is
my command:
"gmx trjconv -f x.trr -s x.gro -o frames.gro"
then it gives me the options to choose my group, but I wanna it choose for
me automatically, as I am going to extract from a lot of
idea.
>
> See also: `gmx mdrun -h` and `gmx grompp -h`.
>
>
> Peter
>
> On 19-09-19 05:13, Hadi Rahmaninejad wrote:
> > Thanks Mehdi,
> >
> > Best,
> > Hadi
> >
> > On Wed, Sep 18, 2019 at 12:38 PM Mahdi Bagherpoor >
> > w
ude the checkpoint file
> from the *NVT* equilibration"
>
> Cheers,
> Mahdi
> On Wed, Sep 18, 2019 at 5:43 PM Hadi Rahmaninejad
> wrote:
>
> > Hello dear users,
> >
> > I am going to run a simulation according to a tutorial, but there is an
> > option
Hello dear users,
I am going to run a simulation according to a tutorial, but there is an
option of "-t nvt.cpt" that I don't know what is it, and I couldn't find
any explanation for that. I appreciate if any of you can give me a short
description of what is that doing,
Best wishes,
Hadi
--
Hello Dear Gromacs users
I need to do umbrella sampling on a single atom. Instead of doing "pulling"
simulation or umbrella sampling, I put a constraint on the atom and after
simulation I got the trajectory of that atom using VMD. The only thing that
I should check is that: Is the constraint in
How did you include your posre.itp into your simulation?
Sent from my iPhone
> On Mar 23, 2019, at 11:39 PM, Neena Susan Eappen
> wrote:
>
> Hello gromacs users,
>
> For the equilibration phase 1, an error message came up following this
> command:
>
> gmx grompp -f nvt.mdp -c em.gro -p
Sorry I forgot to ask this question: did you determine "slab" group in your
.gro file?
On Thu, Mar 21, 2019 at 10:29 AM Hadi Rahmaninejad
wrote:
> Hello Mateusz,
>
> Thank you for your help. However, still I am a little confused. suppose
> that this is the .mdp
gromacs:
> https://www.youtube.com/watch?v=kzJR2_XHkcM
> http://www.mdtutorials.com/gmx/
>
> Best, Mat
>
> On Thu, 21 Mar 2019 at 05:15, Hadi Rahmaninejad
> wrote:
>
> > Hello Mateusz,
> >
> > First of all, I don’t know where should I use these these commands,
for a couple of years now in Verlet
> algorithm.
>
> For reference:
> http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-freezegrps
>
>
> On Wed, 20 Mar 2019 at 15:55, Hadi Rahmaninejad
> wrote:
>
>> Hello dear Gromacs users,
>>
>
Hello dear Gromacs users,
I know how to restrain atoms of an structure solvated in water with force
with option "-DPOSRES". However, for my simulation, I need to exclude
position changing from the simulation, in other words, I need to exactly
fixed them. I highly appreciate if any of you can help
Hello Dear Gromacs Users,
I am doing a simulation in silica structure containig Si and O atoms with
special VDW and charge parameters. My purpose is to separate each Si and O
and consider each of them as one residue, so I don't need to worry about
"Bonded" parameters, only need to define new
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