Hello all,
I created a graphene sheet and performed energy minimization, after energy
minimization I found that parts of the graphene sheet was moved from the
box bottom to the box topside at the same place (as if it was translated
upwards). I looked online for the problem and I understood that I
Hello all,
I created a graphene sheet and performed energy minimization, after energy
minimization I found that parts of the graphene sheet was moved from the
box bottom to the box topside at the same place (as if it was translated
upwards). I looked online for the problem and I understood that I
Hello everybody
I have been using GROMACS 2018.1 in the last month and I got an error "core
dumped" while running the simulation. Accordingly, I have installed the
2020.1 version and while I am doing pressure equilibration (npt), I had the
same error again (I paste it below) which is core dumped.
Hello everybody :)
I want to know how to simulate a graphene sheet in GROMOS 54A7 and get the
.top file knowing that I have the .itp file.
Thanks
Mohamed
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bra...@nitk.edu.in>
wrote:
> Hi,
> What .itp file you have ..
>
> On Tue 4 Feb, 2020, 4:44 PM Mohamed Abdelaal,
> wrote:
>
> > Hello everybody :)
> >
> > I want to know how to simulate a graphene sheet in GROMOS 54A7 and get
> the
> > .top fil
Hello All,
I want to create a graphene sheet with a specific dimensions (10*15*0.284)
nm.
I created a .gro file as below ( as mentioned in this website
https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/
)
GRM: 1 1
, Feb 19, 2020 at 10:10 Alessandra Villa <
alessandra.villa.bio...@gmail.com> wrote:
> HI,
>
>
>
> On Wed, Feb 19, 2020 at 10:31 AM Mohamed Abdelaal
> wrote:
>
> > Many thanks Alessandra for your reply :)
> >
> > gmx solvate will add water a
that :) ?
Thanks,
Mohamed
On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa <
alessandra.villa.bio...@gmail.com> wrote:
> Hi
>
> On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal
> wrote:
>
> > Hello All,
> >
> > I want to create a graphene sheet with a spe
e appropriate
> temperature and adds those velocities to the atoms in your .gro file.
>
> Perhaps there is an easier way that someone can shed some light on, but
> that's what immediately comes to mind.
>
> - John
>
> >
> >
> > On Wed, Mar 11, 2020 at 7
the molecules and
the velocities of the ATOMS were sampled from a distribution with standard
deviation =xx and mean = xxx.
On Wed, Mar 11, 2020 at 7:05 PM Justin Lemkul wrote:
>
>
> On 3/11/20 9:56 AM, Mohamed Abdelaal wrote:
> > I want to insert an atom with a velocity moving d
Hello everybody,
I am trying to insert molecules into a box but I have to insert one single
molecule at a time reaching 3000 molecule in total. Is there a way to
automate this process ?
Thanks
Mohamed
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Gromacs Users mailing list
* Please search the archive at
I want to insert an atom with a velocity moving downwards toward the
graphene sheet in my box.
Yes I need to remove any atom moving away from my substrate or the
deposited atoms and far by 0.4 nm.
Then repeat the process until I have inserted 3000 atoms.
Thanks for your reply.
Mohamed
On Wed,
r 7, 2020 at 3:38 PM Mohamed Abdelaal
> wrote:
>
> > No, I use the generate velocity option in the .mdp files.
> >
> > However I want now to assign different velocities in the x,y,z
> directions.
> > Which I thought it could only be done through the .gro file, but I do
, Apr 9, 2020 at 04:33 Eric Smoll wrote:
> On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal
> wrote:
>
> > Many thanks for your reply
> >
> > The limitation in the generate velocity using the .mdp file, is that
> while
> > I can generate the velocity fro
Many thanks for your quick reply :)
On Tue, Apr 14, 2020 at 11:09 PM Justin Lemkul wrote:
>
>
> On 4/14/20 4:55 PM, Mohamed Abdelaal wrote:
> > Sorry for writing again in the same topic but I couldn't solve
> > the velocity problem.
> >
> > I am trying to rep
re should I add the
constant to change the mean?
Many thanks,
Mohamed
On Thu, Apr 9, 2020 at 5:00 AM Mohamed Abdelaal
wrote:
> Many thanks for your reply :)
>
> All your language assumptions are true and that is exactly what I wanted
> to communicate, next time I will try t
vely, dump the contents of the tpr and make sure the velocities
> you created were read in.
>
> Do you mean that I should manually edit the .tpr file ? I have tried to
open it with text editor but it can't be open.
> -Eric
>
> On Tue, Apr 14, 2020 at 1:56 PM Mohamed Abdelaal
>
Hello everyone,
If I will add the velocity manually to my system, should I add them before
the energy minimization or after ?
I will do the below steps:
1. insert molecules
2. energy minimization
3. NVT equilibiration
4. NPT equilibiration
5. production run.
should I add the velocity before
gt; coordinates and velocities to the trr at every step and then extract gro
> with velocities from the trr). Then go through the gro file and add a
> constant z-velocity to all the atoms that need it. Then read the edited
> gro file in again and proceed.
>
> -Eric
>
> Sent from my iPhon
in the velocity
generation mechanisms.
Many thanks,
Mohamed
On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul wrote:
>
>
> On 4/6/20 12:16 PM, Mohamed Abdelaal wrote:
> > Hello everybody :)
> >
> > Can I use the gmx insert-molecules to insert molecules in my box wi
Hello everybody :)
Can I use the gmx insert-molecules to insert molecules in my box with
velocities by adding the velocities in the .gro file and insert the
molecules from this .gro file ?
Thanks
Mohamed
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Gromacs Users mailing list
* Please search the archive at
Hello everybody,
If my molecules are moving and I want to add the velocity, should I
generate the velocity through the .mdp file, or should I add the velocities
into my .gro file and insert the molecules?
Thanks,
Mohamed
--
Gromacs Users mailing list
* Please search the archive at
Hello everybody,
Can anybody please help me as I am confused between the Temperature and
Pressure coupling in the different .mdp files.
Can you please tell me what is the difference between the Temperature and
Pressure coupling in the NVT.mdp, NPT.mdp during the equilibration and in
the md.mdp
Hello everybody,
I know that due to periodic boundary conditions the molecules move from one
side of the box to the other side and moves outside the box. I also know
how to use trjconv to solve this problem and I usually do this step at the
end of the simulation. However I have noticed that after
Hello everybody,
In order to solve the PBC at the end I use the command:
*gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol *
followed by:
*gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb*
I want to solve this problem after the energy minimization but I don't have
Hello everyone,
I am simulating the evaporation of non protein molecules on a graphene
sheet. I am using gromos force field and hence the lincs constrain are set
to all-bonds. I have done the energy minimization and NVT
successfully without any warnings. During the NPT equilibiration I got
I am simulating Crystal System (C60 molecules)
Thanks,
Mohamed
On Wed, May 6, 2020 at 1:22 AM Arun Srikanth wrote:
> Are you simulating a crystal or amorphous system?
>
> Arun
>
> On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal
> wrote:
>
> > Hello everybody,
>
Hello everybody,
I have two fundamental questions please.
I have measured the fee volume and I discovered that, the free volume
changes with respect to the time during the production run (different value
for each frame). However I have measured the density but the result does
not change with
Yes I measured both, the density and the free volume using gromacs.
Since the free volume changes with respect to time, shouldn’t the density
also change with time ?
Thanks,
Mohamed
On Wed, May 6, 2020 at 08:23 David van der Spoel
wrote:
> Den 2020-05-06 kl. 01:13, skrev Mohamed Abdel
I started with NVT then NPT then md production run.
Thanks,
Kohamed
On Wed, May 6, 2020 at 10:40 Arun Srikanth wrote:
> Is it an NPT simulation or NVT simulation?
> Arun
>
> On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal,
> wrote:
>
> > Yes I measured both, the density a
or NPT) equilibiration ? I
thought that I must do both of them before I start the final production
run.
Thanks again,
Mohamed
On Wed, May 6, 2020 at 12:50 PM David van der Spoel
wrote:
> Den 2020-05-06 kl. 10:21, skrev Mohamed Abdelaal:
> > Yes I measured both, the density and the fr
rning. I know now that
the problem is only in the graphene sheet.
> Alex
>
>
Thanks,
Mohamed
> On 5/3/2020 6:39 PM, Mohamed Abdelaal wrote:
> > Hello everyone,
> >
> > I am simulating the evaporation of non protein molecules on a graphene
> > sheet. I am using gromos
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