On 12/30/19 11:11 PM, sunyeping wrote:
Hello Justin,
Thank you for your reply.
If I need to prove the repeatability of a phenonmenon (such as the
peptide folding pathway or a conformational transition) in
simulations, is it reasonable to run the production MD several times
and each time
Hello Justin,
Thank you for your reply.
If I need to prove the repeatability of a phenonmenon (such as the peptide
folding pathway or a conformational transition) in simulations, is it
reasonable to run the production MD several times and each time the simulation
is continued for the same NPT
On 12/30/19 10:14 PM, sunyeping wrote:
Dear all,
In the molecular dynamics parameters (.mdp option) section of the Gromacs user guide
(http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html), there is an
introduction of the "gen-vel" option. According to the introduction,
On 12/30/19 1:51 PM, Quin K wrote:
Further to following email, is it OK to do an energy minimization with
Gaussian16 so the molecule is refined before MD simulation with Gromacs?
What would be the purpose? A gas-phase optimized geometry has no
relationship to the pose adopted by a molecule
On 12/30/19 10:05 AM, Quin K wrote:
Hi
I noted when I used Autodock vina for docking and used the converted back
.mol2 file from .pdbqt format, there were a lot of changes in the molecule
than the molecule I initially submitted to Vina for docking. Like the *atomic
charges were different. *
On 12/30/19 12:06 PM, Maryam Sadeghi wrote:
Thank you very much Justin.
Just to confirm, in case of longer polymers can I assign 1 monomer/bead to
different charge groups?
I know nothing about your model, but probably yes. Charge groups are
outdated notions, anyway, and are ignored if
Dear all,
In the molecular dynamics parameters (.mdp option) section of the Gromacs user
guide
(http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html),
there is an introduction of the "gen-vel" option. According to the
introduction, if set to "yes", it will generate
Further to following email, is it OK to do an energy minimization with
Gaussian16 so the molecule is refined before MD simulation with Gromacs?
If such an energy minimization is done should I use DFT ?
Would that affect the orientation at which molecule was docked with
protein?
On Mon, Dec 30,
Thank you very much Justin.
Just to confirm, in case of longer polymers can I assign 1 monomer/bead to
different charge groups?
Maryam
On Mon, Dec 30, 2019, 5:32 AM Justin Lemkul wrote:
>
>
> On 12/30/19 2:53 AM, Maryam Sadeghi wrote:
> > Dear All,
> >
> > I have created a coarse-grain (cg)
Here are some details I gathered over some time and how I overcame the
issue of *slow running gromacs* due to not using all threads in the intel
processor.
* Install according to following videos*
https://www.youtube.com/watch?v=vOJsmtFeSGk
https://www.youtube.com/watch?v=BZNzYt_DUB0
SIMD
Hi
I noted when I used Autodock vina for docking and used the converted back
.mol2 file from .pdbqt format, there were a lot of changes in the molecule
than the molecule I initially submitted to Vina for docking. Like the *atomic
charges were different. *
Is this normal? or is there a way to use
Dear Gromacs-Users,
Is there any update on this issue? I have used the following flags for
version 2019.3
/apps/codes/cmake/3.15.4/bin/cmake ..
-DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 -DGMX_FFT_LIBRARY=fftw3
-DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF
-DGMX_DOUBLE=ON
Dear all,
By using the editconf command, we can build a box for the protein molecule, for
example:
gmx editconf -f complex.gro -o newbox.gro -c -d 1.2 -bt cubic
but how to rotate the molecule in the box? I tried to use "-rotate" option of
the editconf command to do so, but I found
On 12/27/19 6:30 AM, Nashit Jalal 17250017 wrote:
Dear all,
I have a protein with three chains PROA, PROB and PROC. I want to check
inter interactions of PROA, PROB, PROC and SOL by keeping PROC frozen (not
to include intra interactions). I have changes mdp file using the following
On 12/27/19 11:26 AM, sp...@iacs.res.in wrote:
Dear all
I have performed a 400 ns mdrun in GROMACS-2016.3. Due to some
problem the job was crushed then I rerun the simulation using
state.cpt file (this happened few more times). The job is finished now
but when I am trying to process the
On 12/27/19 2:36 PM, Pandya, Akash wrote:
Hi all,
I have a quick question about the value obtained for the SASA calculation on a
per residue basis (-or flag). Is this value the absolute SASA for each residue?
Yes.
-Justin
--
==
Justin A.
On 12/28/19 12:41 PM, Miro Astore wrote:
Hello,
I am new to the gromacs work flow, I come from using NAMD.
An example of what I want to do is place harmonic restraints on a subset of
a molecule, for example all of the CA atoms in a protein backbone. I have
found the genrestr function which
On 12/29/19 2:54 PM, Mark Abraham wrote:
Hi,
I expect that's a hydrogen in an NH3+ group being added as a terminus to
your protein. You might want to tell pdb2gmx to stop trying to help with
the termini, with -ter or -noter.
HA3 isn't a terminal proton in the CHARMM force field so I doubt
On 12/30/19 2:53 AM, Maryam Sadeghi wrote:
Dear All,
I have created a coarse-grain (cg) structure of a polymer containing 49
beads (the atomistic structure contains 193 atoms), each beads has a zero
charge.
I have created the .itp file manually, defining the atom types and the
bonds and
On 12/28/19 2:09 PM, Quin K wrote:
Hi
Which temperature should be used for molecular dynamic simulation of a
human protein?
If we used 300K would that give significantly different results from 310K
MD simulation?
Some argue that since human body temperature is around ~310K MD should be
done
On 12/30/19 5:34 AM, Christos Deligkaris wrote:
dear all,
While running my production run of a small molecule noncovalently bound to
DNA in water, I got the error:
Step 8921600:
Atom 20338 moved more than the distance allowed by the domain decomposition
(0.457738) in direction X
distance
On 12/30/19 5:35 AM, wrote:
Thanks for your answer, though I still can't solve this problem. I guess maybe
there is some bug in the development of drude poparizable field.
You have provided no evidence of a bug. The original problem was the use
of an invalid residue name, and without
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