On 11/11/19 3:58 PM, Daniel Burns wrote:
Thank you!
If I use the coordinates of the center of mass for the spherical restraint,
will the ligand remain restrained to that coordinate if the protein rotates
or translates the binding site away from that original position?
No, that's only
On 11/11/19 10:05 AM, Mijiddorj B wrote:
Dear Prof. Justin,
Thank you very much for your reply. My target polymer is the branched
polyethyleneimine. I copied a figure. I am sorry for furthermore asking. If
I understand correctly, the model compound consists of the last two heavy
atoms and
Farideh,
There appears to be a problem with the topology that you are using for the
molecule that explodes.
Look at the pdb files generated at each time the system has exploded. Work
out which group of atoms are moving too far, then look at the topology
around those atoms to identify where the
Thank you!
If I use the coordinates of the center of mass for the spherical restraint,
will the ligand remain restrained to that coordinate if the protein rotates
or translates the binding site away from that original position? Or am I
going about this wrong? Can I set up that spherical
Dear Prof. Justin,
Thank you very much for your reply. My target polymer is the branched
polyethyleneimine. I copied a figure. I am sorry for furthermore asking. If
I understand correctly, the model compound consists of the last two heavy
atoms and first two heavy atoms along with the
On 11/10/19 2:54 PM, Daniel Burns wrote:
Hello,
I have identified a set of amino acid residues that surround a small
molecule binding site. How would I go about restraining the small molecule
ligand to the center of mass of the surrounding residues? I want the
molecule to be able to bounce
Thank you very much Paul, I got it!
--Original--
From:"ZHANG Cheng"<272699...@qq.com;
Date:Mon, Nov 11, 2019 09:57 PM
Hello,
yes, this is indeed possible (see
http://manual.gromacs.org/current/user-guide/mdrun-features.html#running-multi-simulations
for more information on multi simulations with GROMACS).
It is just the case that the tutorial system is too small to be
correctly distributed with domain
Thank you Paul! I want to use more than one mpi processes for each of the REMD,
would it be possible?
--Original--
From:"ZHANG Cheng"<272699...@qq.com;
Date:Mon, Nov 11, 2019 09:39 PM
Hello,
you have set the -mpi option correctly (I think), but the small test
system used for the tutorial can not be split up over more domains (as
the error message tells you).
The idea of the tutorial are here to run on system for each mpi process.
Are you trying to do the same (and run 12
I am using the same files based onMark Abraham's REMD tutorial, except
using a recent Gromacs version
(gromacs/2019.3).http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
For Stage
Hello @ all GROMACS users,
on December 5th 2019, Christian from core developer team in Stockholm
will give a webinar explaining the different options available in mdp
files, and showing how they influence your simulations.
You can find more information about the event here:
Dear GMX users group
Message 4
> I am using GROMOS 43a force field, I have typed by protein and got the
> ligand file from PRODRG.
*Don't use PRODRG; its topologies are not of sufficient quality for running
MD simulations*.
How to generate ligand topology (GROMOS 43a force field)
Does your
13 matches
Mail list logo
