On Sat, 22 Jul 2017 at 2:47 AM, Justin Lemkul wrote:
>
>
> On 7/21/17 10:56 AM, RAHUL SURESH wrote:
> > It sounds like some internal dihedral problem. Request you, check on it.
> >
>
> How did you deduce that?
Dear Justin
I faced the similar kind of problem. Visualisation Of my trajectory help
Hi,
The g96 format is useful for this purpose.
Mark
On Fri, 21 Jul 2017 23:18 Caro Miguel wrote:
> Thanks, that clarifies it (my bad!).
>
>
> --
> Dr. Miguel Caro
> Postdoctoral researcher
> Department of Electrical Engineering and Automation, and
> COMP Centre of Excellence in Computational N
On 7/21/17 9:58 AM, S M Bargeen Turzo wrote:
In order to do an energy minimization and md simulation is it a must to
create a box around your molecule of interest(whether it be a small or
macro molecule). If so can you please explain why?
Depends on what you want to model. If you want to si
Thanks, that clarifies it (my bad!).
--
Dr. Miguel Caro
Postdoctoral researcher
Department of Electrical Engineering and Automation, and
COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Email: mcar...@gmail.com
Work: miguel.c...@aalto.fi
Website: http://mcaroba.dyn
On 7/21/17 10:56 AM, RAHUL SURESH wrote:
It sounds like some internal dihedral problem. Request you, check on it.
How did you deduce that?
Indeed, conformational sampling may be an issue, so one should check the
internal geometries of the ligands, preservation of various interactions with
On 7/21/17 11:30 AM, Mostafa Javaheri wrote:
Dear gmx users
Does anyone know how a dummy atom with no Van der Waals interactions
(zero sigma and epsilon parameters) and also no mass and charges deals
with other real atoms inside the simulation box? Is that possible a
dummy atom with described
On 7/21/17 4:24 PM, Varvdekar Bhagyesh Rajendra wrote:
Dear Justin,
I attempted to write the energy file (edr file) after performing normal mode
analysis (using integrator = nm), but couldn't find gromacs writing nm.edr file
at the end of the nm analysis similar to the way it writes em.edr a
On 7/21/17 5:11 PM, Caro Miguel wrote:
Hello,
I am trying to extract trajectory data with more decimal places than the
standard. I have been using gmx trjconv with the -ndec option to do this in the
past. I am now using the 2016.3 release and the following command:
gmx trjconv -f md.trr -
Hello,
I am trying to extract trajectory data with more decimal places than the
standard. I have been using gmx trjconv with the -ndec option to do this in the
past. I am now using the 2016.3 release and the following command:
gmx trjconv -f md.trr -s md.tpr -o traj.gro -ndec 5
gives me a t
Dear Justin,
I attempted to write the energy file (edr file) after performing normal mode
analysis (using integrator = nm), but couldn't find gromacs writing nm.edr file
at the end of the nm analysis similar to the way it writes em.edr after energy
minimization. So firstly, is it plausible to w
Dear gmx users
Does anyone know how a dummy atom with no Van der Waals interactions
(zero sigma and epsilon parameters) and also no mass and charges deals
with other real atoms inside the simulation box? Is that possible a
dummy atom with described characteristics get infinitely close to a
real at
It sounds like some internal dihedral problem. Request you, check on it.
On Fri, 21 Jul 2017 at 6:54 PM, Sneha Vishwanath <
snehavishwanat...@gmail.com> wrote:
> @ Justin: I have re-imaged the trajectory with trjconv using and still the
> ligand dissociates from one of the chain but remain bound
Hi David,
Thanks for the quick response. I am looking for a pressure wave in air with
a frequency in GHz. I am looking to see the mechanical behavior of
proteins. By implementing a code, do you mean implementing an external
script (such as a code written in python) and then embedding it into the
c
In order to do an energy minimization and md simulation is it a must to
create a box around your molecule of interest(whether it be a small or
macro molecule). If so can you please explain why?
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Li
@ Justin: I have re-imaged the trajectory with trjconv using and still the
ligand dissociates from one of the chain but remain bound with the other
chain.
@ Gangotri: I am not sure how constraining the bond between protein might
help. Can you please elaborate if possible.
Thanks in advance.
Sne
On 7/21/17 8:56 AM, Sneha Vishwanath wrote:
Dear all
I am simulating a dimeric protein, with each subunit bound to a small
molecule. During the simulation, one of the ligands is dissociating from
the chain and moving all around the chain while the same ligand remains
bound to the chain during
On 7/20/17 8:08 AM, Shraddha Parate wrote:
Hi gmx users!
For polarizable effect, I was setting drude force field in Gromacs
I attempted running Lagrangian Dynamics simulation using Drude force field.
mdp file format was used from the supporting data in below paper.
[2015] Implementation of ex
On 7/20/17 5:27 AM, Sonia Milena Aguilera Segura wrote:
On 7/18/17 1:28 PM, Sonia Milena Aguilera Segura wrote:
Dear GROMACS users,
I am running a 4 nm box of ethanol and once I finished the MD, I got the right T, P, density.
However, I noticed that my energies are odd. After several trials
Hey!
You might want to constrain the bond between the 2 protein chains.
G
*Thank you*
*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
On Fri, Jul 21, 2017 at 8:56 AM, Sne
Dear all
I am simulating a dimeric protein, with each subunit bound to a small
molecule. During the simulation, one of the ligands is dissociating from
the chain and moving all around the chain while the same ligand remains
bound to the chain during simulation. Experiments show that the ligand
bin
On 20/07/17 23:53, Aarushi Bhargava wrote:
I am simulating a protein using gromacs 5.0.2 and want to apply time
varying pressure (preferably sine wave) on it. How should I do it in NEMD?
You would have to code to implement a varying pressure of any sort, but
please think about what kind of phys
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