Hello Bratin,
I used charmm-gui to generate the MD input files and used CHARMM36 as
forcefield.
Then I used gromacs for the MD production run for 100ns.
Once I got the trajectory files, I did the membrane analysis using a tcl
script and gridmat.
I followed the gromacs tutorial starting from the
Dear Stephani,
Can u please tell me how you did the simulation and
what forcefield you used for your system. Did you followed the same
tutorial explained by justin lemkul
On Sun, Sep 16, 2018 at 9:46 PM, Stephani Macalino <
stephanimacal...@gmail.com> wrote:
> Hello,
> I
when I run gmx mdrun -v -deffnm 5e61_pr for pr.mdp file then there is an
error of core dumped.Please suggest what should I do
Step 7, time 0.014 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.041436, max 2.491113 (between atoms 3683 and 3684)
bonds that rotated more than 30
These were the errors until the moment of executing the minimization:
After adding ions grompp:
NOTE 1 [file topol.top, line 37566]:
System has non-zero total charge: -18.99
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
On 9/17/18 9:57 PM, Stephani Macalino wrote:
Hello again,
I have pinpointed the problem I have.
I tried to follow
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
.
But I only used pbc whole, nojump and mol center.
After I used nojump,
Hello again,
I have pinpointed the problem I have.
I tried to follow
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
.
But I only used pbc whole, nojump and mol center.
After I used nojump, the thickness values of my trajectory is stable at
Hello Justin,
Thank you for your suggestions. I will have a try.
Min
On Mon, Sep 17, 2018 at 4:58 PM, Justin Lemkul wrote:
>
>
> On 9/17/18 6:57 PM, Min Wu wrote:
>
>> Hello Justin,
>>
>> Thank you for your reply. But the problem is after even 90ns production
>> simulation, the random coil of
On 9/17/18 6:57 PM, Min Wu wrote:
Hello Justin,
Thank you for your reply. But the problem is after even 90ns production
simulation, the random coil of these two spots never change. The right
helix structure never comes back anymore.
Are you basing this assessment solely on what you see
Hello Justin,
Thank you for your reply. But the problem is after even 90ns production
simulation, the random coil of these two spots never change. The right
helix structure never comes back anymore.
Thank you.
Min
On Mon, Sep 17, 2018 at 4:54 PM, Justin Lemkul wrote:
>
>
> On 9/17/18 6:42
On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote:
Hi everyone.
I'm trying simulate a protein in water followin lysozyme tutorial using
gromacs 2016.3. When triying minimize the system after make the box and
insert a salt concentration the minimization has been stoped sendingme the
On 9/17/18 6:42 PM, Min Wu wrote:
Hi All,
When I use pdb2gmx of gromacs 5.0.7 to convert 2lsb.pdb to gro file, the
initial helix structure of His 177 and His 187 change to coil. I modified
the His to HISD in the original pdb to match the residue name in opls-aa
forcefield. When I change
Hi
Reduce your timestep and see as it is suggested.
Best
On Mon, Sep 17, 2018 at 5:48 PM Mario Andres Rodriguez Pineda <
mand...@iq.usp.br> wrote:
> Hi everyone.
> I'm trying simulate a protein in water followin lysozyme tutorial using
> gromacs 2016.3. When triying minimize the system after
Hi everyone.
I'm trying simulate a protein in water followin lysozyme tutorial using
gromacs 2016.3. When triying minimize the system after make the box and
insert a salt concentration the minimization has been stoped sendingme the
following error:
step 16: One or more water molecules can not be
Hi All,
When I use pdb2gmx of gromacs 5.0.7 to convert 2lsb.pdb to gro file, the
initial helix structure of His 177 and His 187 change to coil. I modified
the His to HISD in the original pdb to match the residue name in opls-aa
forcefield. When I change HISD back to HIS, when viewed in VMD,
On 9/17/18 11:11 AM, BIJENDRA KHADKA wrote:
Hello Everyone,
Recieved an following error while using the CHARMM forcefield for
NAD-protein interaction.
All suitable gromacs topology files for ligand was generated using the the
python script (and procedure) described in the MacKerell website.
Dear all,
To emulate an infinite reservoir of reactive solution, I need to add new
precursor molecules periodically to a region of the simulation box. The
infinite reservoir is a box where for which the equations are not being
solved while the equation are normally being solved for the simulation
Hello Everyone,
Recieved an following error while using the CHARMM forcefield for
NAD-protein interaction.
All suitable gromacs topology files for ligand was generated using the the
python script (and procedure) described in the MacKerell website.
The nad.itp file is attached herewith
Any
4 days after original post without answer at all I think every post is helpful
somewhat. Especially when it encourages discussion and even more answers right
away.
Am I wrong?
On Monday, September 17, 2018, 4:48:52 PM GMT+3, João Henriques
wrote:
I'm sure there's lots of software
I'm sure there's lots of software that can perform that task, I just felt
it was important to underline that a kernel density estimation is what is
needed in this case. If you go back to your original reply, there's nothing
in there that can help the original poster solving his problem.
J
On
Also you can use R for that task. Very easy like:density(x, ...)
On Monday, September 17, 2018, 4:26:38 PM GMT+3, João Henriques
wrote:
How does that reply the OP's question? To calculate the joint probability
distribution you need to perform a kernel density estimation. I'd recommend
How does that reply the OP's question? To calculate the joint probability
distribution you need to perform a kernel density estimation. I'd recommend
either SciPy or Seaborn if you're not averse to coding in Python:
Hi all,
I have carried out PCA on my MD trajectories. I want to investigate the
frequency distribution of my MD trajectory projected on Principle Component
modes (PC1, PC2 etc.). I ultimately want these frequencies as function of time
using Fourier Transform. Is there any Gromacs utility that
On 9/17/18 8:50 AM, Rakesh Mishra wrote:
In my above protocol,
What I found that, my system (12 dsDNA) placed with their helical axis is
along the X axis (in VMD we checked ).
If the helix rotates, your application of a bias only along x becomes
invalid or will do something you don't
In my above protocol,
What I found that, my system (12 dsDNA) placed with their helical axis is
along the X axis (in VMD we checked ).
When I am applying pulling on r_12 ( with pull_coord1_dim = Y N N
). Keeping r_24 as a reference group (not fixed).
Distance between both group is
Gromacs xvg files can be opened with Xmgrace and you should get plot out of
them right away then. I am not sure that those plots fit your need but you can
edit them with same program right away.Xmgrace is probably available over your
Linux distribution package manager like "sudo apt-get
On 9/17/18 8:37 AM, Vytautas Rakeviius wrote:
And what about OPLS-AA/L if I do nvt equilibration of my protein in water
with it is it OK to do constraints = all-bondsall the time like I
am used to do?
I would encourage you to examine the primary literature for the force
And what about OPLS-AA/L if I do nvt equilibration of my protein in water with
it is it OK to do constraints = all-bondsall the time like I am
used to do?
On Monday, September 17, 2018, 3:18:51 PM GMT+3, Justin Lemkul
wrote:
On 9/17/18 8:12 AM, Vytautas Rakeviius
On 9/17/18 8:25 AM, Rakesh Mishra wrote:
Agreed with this
"Newtonian mechanics always apply, but it's not as simple as "pull on X,
and Y moves." Your system evolves under the influence of the biasing force."
Perhaps my nomenclature was bad here - X and Y are not Cartesian
directions, they
Agreed with this
"Newtonian mechanics always apply, but it's not as simple as "pull on X,
and Y moves." Your system evolves under the influence of the biasing force."
The same I am saying that on Pulling X, X will fell equal and opposite but
not Y and Z.
Meaning ,
If 3' of one strand will
Can you explain more to us when it is not appropriate to constrain all bonds
during nvt equilibration?
On Monday, September 17, 2018, 3:06:56 PM GMT+3, Justin Lemkul
wrote:
On 9/17/18 8:04 AM, Vytautas Rakeviius wrote:
> I think your attachment to email was lost during re-transfer
On 9/17/18 8:04 AM, Vytautas Rakeviius wrote:
I think your attachment to email was lost during re-transfer and it would be
nice to see that, but I think what you need is:constraints =
all-bondsIn that mdp file.
That depends on the force field convention. It is not
I think your attachment to email was lost during re-transfer and it would be
nice to see that, but I think what you need is:constraints=
all-bondsIn that mdp file.
On Friday, September 14, 2018, 4:07:43 PM GMT+3, Gonzalez Fernandez,
Cristina wrote:
Dear Gromacs
On 9/17/18 4:52 AM, Rakesh Mishra wrote:
Agreed.
But, I could not solve.
So Justin, If I pull 3' end of one strand of DNA by taking as
3' end of the complimentary strand as a reference group (Note that
I have not fixed or not made it immobile ) then according to the theory of
newtons third
What is your system composed of? It is generally a good idea to couple
solvent and solute separately (as long as solute is "big enough", see
http://www.gromacs.org/Documentation/Terminology/Thermostats), so Vytautas
reply isn't the best advice. It will solve your problem, but that's
generally not
Hi!
There are two key points here.
1) Index groups don't have to be mutually exclusive. So, you can have your
20+ indices, but also have an inclusive index that encompasses more or all
of your atoms, which you can then use for tc (or comm removal, etc.). The
only necessary thing is that the
Without going into details and setting:
tc-grps = System
should allow to proceed without fatal errors.
On Monday, September 17, 2018, 1:58:50 PM GMT+3, Sebastian Muraru
wrote:
Hi there! I am a Masters student and this is my first email to the list. I
would just like to ask whether
Hi there! I am a Masters student and this is my first email to the list. I
would just like to ask whether someone can clarify something for me regarding
the index .ndx files.
I am using an nvt.mdp file in order to run an nvt equilibration step. The
section of interest is the following
I suggest this tool:https://github.com/llazzaro/acpype
On Friday, September 14, 2018, 10:44:56 PM GMT+3, SAKO MIRZAIE
wrote:
Hi every one,
I need the topology parameters for pyridoxal phosphate linked to lysine
with amber99sb force field. does anyone have the mentioned parameters? I
Agreed.
But, I could not solve.
So Justin, If I pull 3' end of one strand of DNA by taking as
3' end of the complimentary strand as a reference group (Note that
I have not fixed or not made it immobile ) then according to the theory of
newtons third law reference group (which is not immobile or
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