Hello,
I try to visualize a .gro file from Martini simulation. However, I
noticed that the lipids always above the water molecule and my protein
split into two. Even after I run the following command:
gmx trjconv -s dppc-md.tpr -f dppc-md.gro -pbc whole -dump 0 -o
dppc-md-pbc.gro
The
Dear Tsjerk
Thanks for your reply.
I think that there is another problem, except for visualization.
I obtained the Z coordinate (along the bilayer normal) of the center of
mass of the 4 drug molecules (violet, blue, red and green lines) and
DPPC lipid bilayer (black line) as a function of
On 9/15/14 4:52 AM, shahab shariati wrote:
Dear Tsjerk
Thanks for your reply.
I think that there is another problem, except for visualization.
I obtained the Z coordinate (along the bilayer normal) of the center of
mass of the 4 drug molecules (violet, blue, red and green lines) and
DPPC
Dear Justin
Very very thanks for your time and consideration.
Excuse me for many questions.
I want to make sure my trajectory is valid and accurate for analysis and
then for writing related paper.
My last question is that can I use this trajectory for doing analysis such
as
g_traj, g_dist,
On 9/15/14 12:11 PM, shahab shariati wrote:
Dear Justin
Very very thanks for your time and consideration.
Excuse me for many questions.
I want to make sure my trajectory is valid and accurate for analysis and
then for writing related paper.
It is.
My last question is that can I use
Dear Justin
Thanks for your answer.
You said The raw output of g_traj in this case is not very useful
I want to know position and location of drug molecules relative to the DPPC
bilayer during simulation time.
In your opinion, how should I use this tool (g_traj)?
Is g_dist appropriate for
On 9/15/14 3:12 PM, shahab shariati wrote:
Dear Justin
Thanks for your answer.
You said The raw output of g_traj in this case is not very useful
I want to know position and location of drug molecules relative to the DPPC
bilayer during simulation time.
In your opinion, how should I use
On 9/13/14 7:59 AM, shahab shariati wrote:
Dear Justin
you said The -trans option takes a vector where you specify the amount of
translation to apply
I do not know what vector should be considered in -trans option.
Well, what have you tried? You need to shift your system along z, the
Dear Justin
Thanks for your reply.
I inserted 4 drug molecules in close vicinity to the membrane surface
in water phase, in one side of bilayer (for example, top). In the
different frames of trajectory, some of drug molecules (one or two
drug molecules) are seen in other side of bilayer
On 9/14/14 8:43 AM, shahab shariati wrote:
Dear Justin
Thanks for your reply.
I inserted 4 drug molecules in close vicinity to the membrane surface
in water phase, in one side of bilayer (for example, top). In the
different frames of trajectory, some of drug molecules (one or two
drug
Dear Justin
I did MD simulation on the NPT ensemble:
pcoupl = Berendsen
pcoupltype = semiisotropic
ref_p = 1.0
In this condition, to solve this problem, what should I do?
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On 9/14/14 8:58 AM, shahab shariati wrote:
Dear Justin
I did MD simulation on the NPT ensemble:
pcoupl = Berendsen
pcoupltype = semiisotropic
ref_p = 1.0
In this condition, to solve this problem, what should I do?
I have already
Dear Justin
I did following:
trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9
Based on your reply*, *I translated all system along the z.
I used x and y according to box dimension.
I used 9, instead of z dimension (8.30034), for z.
When I see **.xtc using vmd, problem
On 9/14/14 9:52 AM, shahab shariati wrote:
Dear Justin
I did following:
trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9
Based on your reply*, *I translated all system along the z.
I used x and y according to box dimension.
I used 9, instead of z dimension
On 9/14/14 10:29 AM, shahab shariati wrote:
Dear Justin
Based on your previous reply, I used following:
trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -pbc mol –trans 0 0 7
When I see **.xtc using vmd, unfortunately, problem was not solved.
Please see the following link:
Hi,
Just a small side note. There's nothing intrinsically nonsensical about
translating more than a box size. The PBC are translation invariant, so you
can do anything and have the system be fine. However, for visualization,
translating one box length, and put the stuff back in the box, makes as
Dear Justin
you said The -trans option takes a vector where you specify the amount of
translation to apply
I do not know what vector should be considered in -trans option.
please guide me to solve this problem as soon as possible.
Best,
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Dear Gromacs users
Unfortunately, no one did not answer my previous question about
selection of appropriate option for trjconv -pbc to solve pbc problem.
For preparation of initial system, I inserted 4 drug molecules in
close vicinity to the membrane surface in water phase, in one side of
On 9/11/14 8:01 AM, shahab shariati wrote:
Dear gromacs users
When I see trajectory file using vmd, there is state showed in following link:
https://www.dropbox.com/s/g8i934atodrb7te/figure2.TIF?dl=0
in initial structure, all 4 drugs were inserted in water phase, in one side of
bilayer.
Dear Justin
Very thanks for your answer.
Unfortunately, I am beginner in MD simulation of bilayer membrane systems.
Based on your answer (You can try the translation options of trjconv in
conjunction with -pbc mol), should I use following command?
trjconv –trans –pbc mol
trjconv –pbc nojump
Dear Michael Carter
Thanks for your answer.
I used
-pbc nojump
Followed by -fit rot+trans
Unfortunately, my problem was not solved.
Please guide me to solve this problem.
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Dear gromacs users
I did MD simulation of my system containing DPPC lipids + water molecule
and 4 drug molecules.
I saw trajectory file using VMD.
Unfortunately, drug molecules jump across the box.
How to resolve this PBC problem?
which of -pbc options (none, mol, res, atom, nojump, cluster
Hi,
Try -pbc nojump
Best,
Mike
On 09/09/2014 15:11, shahab shariati shahab.shari...@gmail.com wrote:
Dear gromacs users
I did MD simulation of my system containing DPPC lipids + water molecule
and 4 drug molecules.
I saw trajectory file using VMD.
Unfortunately, drug molecules jump across
Also if you want to fix the position on the centre of mass (no rotating or
translating) try
-pbc nojump
Followed by -fit rot+trans
Remember to use you new .xtc from your no jump command for the -fit
command. Then view in vmd and your molecules will not jump, rotate, or
translate around the box.
dear gromacs users
i did simulate zinc and copper ion on human growth hormone protein
when i saw my md.gro and md.xtc files by VMD software
i found out my system isn,t in the box(cubic)
i tried to solve this problem by :
trjconv -f md.xtc -s md.tpr -o new.xtc -n index.ndx -pbc mol
but there is
Hi all,
I am aware of that this topic has been discussed for many times. However, I
need your more guidance whether I am experiencing PBC problem after MD or
not.
My MD box has enzyme+ligand+coenzyme complex. As I have already wrote to
the user list, I am using the force field parameters from
If there's a problem, trjconv can handle it with the use of the right index
groups, as suggested at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
But it can't keep these three things together if there's no index group
that describes these three things. You may need
Dear Kannan,
Thank you for your fast response. The problem is that the ligand is as far
as 16 Ang., which is too far away from the coenzyme for any kind of bonding.
here is the link for downloading my dist.jpeg file.http://we.tl/ACencjievC
Do you think that this is a real PBC problem?
Really
Dear Justin and Tsjerk
you said Some tools handle PBC properly, some don't .
I want to know exactly which tools of gromacs handle PBC properly.
Can I find these tools in manual?
I did simulation of a system containing protein and cnt using gromacs 4.5.6.
When I see trajectory by VMD, in some
On 2/2/14, 7:15 AM, Atila Petrosian wrote:
Dear Justin and Tsjerk
you said Some tools handle PBC properly, some don't .
I want to know exactly which tools of gromacs handle PBC properly.
Can I find these tools in manual?
No, because it's not possible to test every single command that
Dear Gromacs users
I did simulation of a system containing protein and cnt using gromacs 4.5.6.
When I see trajectory by VMD, in some frames, protein atoms exit one side
of box
and enter opposite side of box (pbc problem). I know I should use -pbc
option of
trjconv tool. But I do not know
Hi,
trjconv -s topol.tpr -f traj -pbc mol -o traj_modified
select '0' for the entire system
You can try using either 'mol' or 'nojump' depending on your visualization
needs.
cheers,
Tarak
On Wed, Jan 29, 2014 at 3:39 PM, Atila Petrosian
atila.petros...@gmail.comwrote:
Dear Gromacs users
I
Dear kannan
Thanks for your reply
Are you sure there is not pbc problem in my case.
For example, can I do g_dist tool to obtain distance between protein and
cnt? Is output for g_dist true and rational?
Best wishes
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Daer kannan
Thanks for your reply
Picture relating to g_dist is in the following link:
https://www.dropbox.com/s/c86ubhdguy9ai8b/g_dist.bmp
Distance between protein and cnt was increased in during 1000-2500 ps,
exactly those
frame are unusaul in VMD (in my opinion, pbc problem).
Best wishes
--
Dear Justin
Thanks for your reply.
To obtain modified trajectory and then comparing with original trajectory,
I do not know exactly which of none, mol, res, atom, nojump, cluster or
whole is appropriate for me.
Best wishes
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On 1/29/14, 9:13 AM, Atila Petrosian wrote:
Dear Justin
Thanks for your reply.
To obtain modified trajectory and then comparing with original trajectory,
I do not know exactly which of none, mol, res, atom, nojump, cluster or
whole is appropriate for me.
In a simple case like this, many
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