Hi,
I have visualized the molecules in vmd and these two water molecules are
placed diagonally opposite in the box. So, in that case obviously, the
distance will be greater than the box length. And the two water molecules
are within the box only.
And yes, my box here is cubic.
Thank you.
[imag
Hi,
Only if the box is cubic.
Mark
On Tue, Jun 5, 2018 at 3:20 AM Quyen V. Vu wrote:
> Hi Dillip,
> As Mark suggest, If you want to calculate by your own code, you can put the
> condition to check which is the nearest neighbour by comparing with box
> length/2
>
>
> On Mon, Jun 4, 2018, 19:42
Hi Dillip,
As Mark suggest, If you want to calculate by your own code, you can put the
condition to check which is the nearest neighbour by comparing with box
length/2
On Mon, Jun 4, 2018, 19:42 Mark Abraham wrote:
> Hi,
>
> You have a periodic cell, so in general the distance from A to the nea
I am including orientation restraints in my md simulation for N-H vectors, how
can I test RDC fitness to test if my simulation is actually doing what is
expected of it?
Thank you for your help
Hanin
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Hi,
I do not do an mdrun -rerun. I think that I can not do it, since I have
a trajectory with protein only. And I aimed to have a trajectory with
the protein, water, and ions. Do I misunderstand something?
On 06/04/2018 10:45 PM, Mark Abraham wrote:
Hi,
On Mon, Jun 4, 2018 at 10:40 PM Tama
Hi,
On Mon, Jun 4, 2018 at 10:40 PM Tamas Hegedus wrote:
> Hi,
>
> I have to rerun a simulation done in gmx 5.1.4 to save also the water
> and ions.
>
> First, I took the equilibrated gro and the modified mdp to generate the
> input tpr for the production run using gmx 2018.1. The results are
>
Hi,
I have to rerun a simulation done in gmx 5.1.4 to save also the water
and ions.
First, I took the equilibrated gro and the modified mdp to generate the
input tpr for the production run using gmx 2018.1. The results are
significantly different (I think that this is ok). But I would like t
Is there any suggestion about how can i make this system in least box size?
with periodic boundary condition in all dimensions?put NT in middle or at
z=0?
Best
-Rose
On Mon, Jun 4, 2018 at 2:19 PM, rose rahmani wrote:
> It's ZnS and yes it's periodic and in water not in vaccum. I used DFT just
On 6/4/18 1:35 PM, Apramita Chand wrote:
Dear Justin,
Thanks for your reply
You're right. I should be choosing a particular density level for all the
components.
There's another doubt. Why Is it necessary to center the protein before
doing g_spatial?
You need a frame of reference for the out
Dear Justin,
Thanks for your reply
You're right. I should be choosing a particular density level for all the
components.
There's another doubt. Why Is it necessary to center the protein before
doing g_spatial?
Thanks
Apramita
On 6/4/18 12:04 PM, Apramita Chand wrote:
> Dear Justin,
> Thanks for
On 6/4/18 12:04 PM, Apramita Chand wrote:
Dear Justin,
Thanks for your reply.
I followed your suggestion and generated the output for urea SDF
(gride_urea.cube) and water SDF(grid_water.cube).
When I visualise both together, I get a picture that is attached in the
link as follows:
https://driv
On 6/4/18 1:20 PM, Samieegohar, Mohammadreza wrote:
Hi Kevin
The nanoparticle is fixed in the middle of box and is not in the edge.
I used PBC boundary condition
Is it because of water freezing ?
Voids observed during NVT are generally due to setting up an initial box
that is too large f
Hi Kevin
The nanoparticle is fixed in the middle of box and is not in the edge.
I used PBC boundary condition
Is it because of water freezing ?
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Kevin Boyd
Sent: Monday, June 4, 2018 12:
Hi,
Why would you want to "ruin" a perfectly good nanoparticle? :)
Could this be a visualization artifact? What kind of treatment of
periodic boundary conditions are you applying prior to visualization?
If you use a PBC option that makes your nanoparticle contiguous and
not split across periodic
Hello
I am ruining a nanoparticle inside water. I use coarse grained model for water
and nanoparticle
My problem is:
When I run the system in NVT 298K , after some steps there is a empty area
inside the water (like a hole) while the initial structure has a good
distribution for water molecules
Dear Justin,
Thanks for your reply.
I followed your suggestion and generated the output for urea SDF
(gride_urea.cube) and water SDF(grid_water.cube).
When I visualise both together, I get a picture that is attached in the
link as follows:
https://drive.google.com/open?id=1lTF-0pSG4-6p0dQ2W7IQWPiz8
Dear Gromacs users,
I am using Gromacs 5.0.6 with CHARMM27 forcefield. I want to do FEP analysis
and I did it based on this tutorials:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html
.
But I just want to peturb some atoms of the protein, howeve
Hii
Thank you for your help. It is working successfully.
Sunipa
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On 6/4/18 8:57 AM, SHAHEE ISLAM wrote:
hi,
i am doing thr rmsd calculation of protein,by using the command
gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic.tpr -f
../pbc.xtc/md-0-1.xtc -o rmsd-p1-0-1.xvg -tu ns (this is for first 1
microsecond)
then again i have done for the next 1 micro sec
hi,
i am doing thr rmsd calculation of protein,by using the command
gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic.tpr -f
../pbc.xtc/md-0-1.xtc -o rmsd-p1-0-1.xvg -tu ns (this is for first 1
microsecond)
then again i have done for the next 1 micro second
gmx rms -n ../ndx/index-p1-0-1.ndx -s ..
On Mon, Jun 4, 2018 at 1:10 PM, wrote:
> Hii
>> I have tried installation of do_x3dna in ubuntu system following the
>> instructions given in the link. Installation done successfully then I
>> have written the path of do_x3dna in .bashrc file(export
>> do_x3dna=/usr/local/do_x3dna/bin/) and sourc
Hi,
Trjconv -pbc mol is documented to do a particular thing.
If that's not what you want, even though it may have coincidentally done
what you wanted on some other trajectory, then please reconsider that
choice.
If it's not doing what it says, it would be good to see some more detail
than "it do
Hi,
You have a periodic cell, so in general the distance from A to the nearest
periodic image of B is across a cell boundary. Trjconv cannot produce a
trajectory so that all pairs of A and B will have a non-periodic distance
that is the minimum distance. Use a tool that already understands this,
l
I think you should check as others did ex.: Optimization of the OPLS-AA Force
Field for Long Hydrocarbons J. Chem. Theory Comput., 2012, 8 (4), pp 1459–1470
On Monday, May 28, 2018, 8:23:50 PM GMT+3, Atila Petrosian
wrote:
Hi all,
I want to do md simulation of oil hydrocarbon?
Is t
On 6/4/18 7:05 AM, Apramita Chand wrote:
Dear All,
I want the SDF of urea as well as water molecules around my peptide
molecule. For this purpose , I used trjconv to get traj1.xtc with -fit
rot+trans option(selecting peptide as fitting option and system as output).
Using this traj1.xtc, I gene
On 6/4/18 6:13 AM, Anjana Jayasinghe wrote:
Dear Gromacs Users,
Is there any difference in the simulation, if we define the spc.itp as,
| #ifdef FLEX_SPC |
| | #include "flexspc.itp" |
| | #else |
| | #include "spc.itp" |
| | #endif |
instead of using the single line #include "spc.itp"
On 6/4/18 4:19 AM, Quyen V. Vu wrote:
Hi,
As i know that vmd cannot understand dodecahedron, he will take 3 numbers
and plot a cubic while your box still is dodecahedron
VMD will display whatever coordinates it is given. GROMACS will, by
default, write coordinates using a triclinic represe
On 6/3/18 8:50 AM, delara aghaie wrote:
Dear Gromacs users
I want to calculate the angle between P-N vector in the head group of DPPC
molecules with the z-axis (bilayer normal) using gangle command.I know that for
the z axis I should use (-g2 z) but do not know how to define a vector for P
Hello all,
I have extracted the trajectory of my system containing all the water
molecules and my box length is 2.48 ~2.5 nm.
The command was:
gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o nptmdtrjwater500.gro -dt
60 #i have 6 frames (30ns is the time and saved the coordinates
for 0.5
On 6/3/18 7:55 AM, m g wrote:
Dear Justin,I fellow your tutorial " Umbrella Sampling", I want to pull a protein across
the membrane but I don't know how set the "define" section.
What you need to do does not require any special restraints. See
previous posts on this topic. The restraints us
Hello all,
I have extracted the trajectory of my system containing all the water
molecules and my box length is 2.48 ~2.5 nm.
And i have written a code which calculates the inter-atomic distance (in my
case it is inter oxygen distances). And when i calculate it (using the
distance formula ie.,
{sq
- Message from rajendra kumar -
Date: Mon, 4 Jun 2018 12:23:56 +0200
From: rajendra kumar
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Groove width
To: Discussion list for GROMACS users
I am doing simulation of DNA molecule. I want to calculate groove wi
Hii
I have tried installation of do_x3dna in ubuntu system following the
instructions given in the link. Installation done successfully then I
have written the path of do_x3dna in .bashrc file(export
do_x3dna=/usr/local/do_x3dna/bin/) and source the file source ~/.bashrc.
Then I tried doing do_x3d
Hi all
I want to center my molecule into a rectangular box after final mdrun by
GROMACS. I am using the following command:
gmx trjconv -f traj.trr -s md.tpr -center -pbc mol -b 100 -e 120 -o
test.gro
But output shown is still out of the box. This command works for cubic
box. Is there anything
Dear All,
I want the SDF of urea as well as water molecules around my peptide
molecule. For this purpose , I used trjconv to get traj1.xtc with -fit
rot+trans option(selecting peptide as fitting option and system as output).
Using this traj1.xtc, I generated traj2.xtc with centering the peptide and
>
>
> I am doing simulation of DNA molecule. I want to calculate groove width of
> DNA in GROMACS. How to do this? Someone please help.
>
>
You may use do_x3dna (http://do-x3dna.readthedocs.io). It uses 3DNA in
background and works with GROMACS files. Package also includes tools to
analyze the la
Dear Gromacs Users,
Is there any difference in the simulation, if we define the spc.itp as,
| #ifdef FLEX_SPC |
| | #include "flexspc.itp" |
| | #else |
| | #include "spc.itp" |
| | #endif |
instead of using the single line #include "spc.itp" ?
Can anyone help me to understand the differenc
It's ZnS and yes it's periodic and in water not in vaccum. I used DFT just
for optimization and obtaining charges. I did this job for an slab before.
I mean the AA was between slab surface and wall but it was the vaccum space
before slab and after wall. imagine this structures in a box of z=12. Th
It's a bit unclear what's happening in your system. Are you simulating
in vacuum, or in solvent? I am assuming it's in solvent and that the
word "vacuum" simply means space unoccupied by the structure, i.e. a
term used by DFT folks. With all nanotubes (carbon, ZnS, BN, etc), water
forms various
Sorry i should correct myself
On Mon, 4 Jun 2018, 13:10 rose rahmani, wrote:
> I have nothing to say...
> but i'm a beginner and i comment here to have your ideas as experienced.
> It's not CNT. It's an inorganic nanotube which its partial atomic charges
> (0.48 , -0.48) is calculated by DFT.
>
I have nothing to say...
but i'm a beginner and i comment here to have your ideas as experienced.
It's not CNT. It's an inorganic nanotube which its partial atomic charges
(0.48 , -0.48) is calculated by DFT.
When i optimized structure in other packages i put it in box with Z=3. So
first i have b
Hi all
I want to center my molecule into a rectangular box by GROMACS. I am using
the following command:
gmx trjconv -f traj.trr -s md.tpr -center -pbc mol -b 100 -e 120 -o
test.gro
But output shown is still out of the box. This command works for cubic
box. Is there anything different flag fo
Hii David
I want to see if there is any change in the groove width in presence
of different solvents. I thing this can give me some information of DNA
structural change if it is happening in that particular solvent.
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Hi,
As i know that vmd cannot understand dodecahedron, he will take 3 numbers
and plot a cubic while your box still is dodecahedron
On Fri, Jun 1, 2018, 06:48 Seketoulie Keretsu wrote:
> Dear All,
>
> I am doing he Protein-ligand complex tutorial on gromacs 5.0.7 (newly
> installed). I have suc
Thank you for your suggestion. This is a new thing I am learning.
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I will be using more smileys, I promise -- especially given how often I
post. You know how wrong Landau was when he said: "Doing science out of
politeness always results in complete lack of science AND politeness." A
rude person that guy was!
By the way, those postdocs, they should check out t
Hi,
Let's be clear - so called common sense is the product of experience, and
new people should not be expected to have it. They can be expected to have
tried to solve their own problem :-) The first part of your answer looks
like it addressed your frustration, not the question. Your actual answer
I'm kind and civil, practically a sweetheart. I just can't put smiley
faces everywhere! On the other hand, it does not hurt to try things and
have a little bit of initiative. I don't know why I am telling you this,
like you've never supervised students... Also, CNTs are simulated
exactly the sa
Hi,
Let's keep the discussion kind and civil, please. What's obvious when you
have experience often isn't when you are new. :-) I sure don't understand
the arithmetic involved, but then I've never attempted a CNT simulation!
Mark
On Mon, Jun 4, 2018, 09:08 Alex wrote:
> And again, your questio
And again, your question has nothing to do with Gromacs. It has to do
with what you want to do, common sense, and basic arithmetic.
CNTs interact at pretty short range (if they are intact and without edge
passivation), so I'd just go with a distance sweep range of ~1.5 nm and
give it some addi
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