Did you look at the coordinate file using vmd or pymol and the
atoms/molecules noted by the error?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
Moreover, this protein has ATP molecule also meaning it is a three molecule
complex.
On Tue, 22/1/19, Dr. Seema Mishra wrote:
Subject: Re: [gmx-users] RMSD plots protein-protein complex
To: gmx-us...@gromacs.org
Date: Tuesday, 22 January, 2019,
I am also interested in answers to this thread. Can a protein only plot in a
protein-peptide complex have increasing backbone RMSD values at 100 ns of
simulations? If no, what needs to be done to stabilize trajectory?
On Sun, 20/1/19, Justin Lemkul
Hi, everyone,
We are simulating a pure DPPC bilayer with 128 lipids.
Now, we defined a box around the bilayer, and solvated, after solvating, we
removed water molecular between the bilayer.
Then, we did energy minimization for the system. However, when we got our
nvt.tpr file, and did NVT
I also tried to reduce the "emtol" gradually in the mdp file, i.e. from 1000 to
100 to 10. It passed the "emtol = 1000" but it stopped again at "emtol = 100",
i.e. outputting dozens of pdb files before the "LINCS warnings".
Then I looked at the edr files.
The potential in "emtol = 1000" and
Hi Gromacs folks,
I am trying to simulate protein and ligand compound.
I did several 200 ns simulations and combined them into one trajectory file
with the commands:
gmx trjcat -f md_round1_10-200ns.xtc
md_round2_10-200ns.xtcmd_round3_10-200ns.xtc -o md_combined.xtc -cat
-settime
I set the
I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was told
"Too many LINCS warnings" in the minimization after solvation with
coarse-grained waters.
I try to diagnose the problems based on
http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up
The total potential energy of the system is printed when you use g_energy
(in your version)
See Justin tutorial for example:
http://www.mdtutorials.com/gmx/lysozyme/05_EM.html
Best,
On Mon, Jan 21, 2019 at 3:28 PM Indu Kumari wrote:
> Good evening sir,
>
> Did you use this command?
>
>
Hi all,
My point is when you center your solute at (0,0,0) there is a half of your
solute will be placed at the quarter of negative coordinates. And then you
add water, gmx solvate will only add water in positive coordinate region.
Am I right?
On Wed, Jan 16, 2019 at 5:19 AM Omkar Singh
wrote:
Good evening sir,
Did you use this command?
g_energy -f em.edr -o em.xvg
When should I meet you sir, tomorrow?
With regards,
*Indu Kumari*
On Mon, Jan 21, 2019 at 12:23 PM Rituraj Purohit
wrote:
> Hi Friends,
> How to get a "graph of potential as function of time" ?? Currently I am
>
Hi,
why don't you use gmx energy?
GROMACS online documents said: "gmx potential computes the electrostatical
potential across the box"
On Mon, Jan 21, 2019 at 7:53 AM Rituraj Purohit
wrote:
> Hi Friends,
> How to get a "graph of potential as function of time" ?? Currently I am
> using gmx
Hi
Can anyone guide me on genertaing sim extended file in gromcas to be used
in SIMtoEXP software.
--
*Best Regards*
Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
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