Hi,
I am trying to do a simple simulation in GROMCAS 2018.6, of a protein in
tip3p water with the amber99 forcefield. Its a 14nm cubic box with two
protein chains, and 87651 water molecules, 269525 atoms total. I am able to
energy minimise to an Fmax < 500, and then perform nvt and npt
equilibriati
On 12/1/16 1:23 PM, abhisek Mondal wrote:
Hi,
I'm constantly getting a strange error of system blow up during
equilibration procedure. I'm relatively new to gromacs, please help me to
get my things straight.
I have a ligand bound protein structure in solvated condition.
So, I was using:
gmx m
Hi,
I'm constantly getting a strange error of system blow up during
equilibration procedure. I'm relatively new to gromacs, please help me to
get my things straight.
I have a ligand bound protein structure in solvated condition.
So, I was using:
gmx mdrun -v -deffnm em #for minimization
Upon suc
Thank you Justin.
Sent from my iPhone
> On Jul 13, 2016, at 8:13 AM, Justin Lemkul wrote:
>
>
>
>> On 7/13/16 9:12 AM, Deep Bhattacharya wrote:
>> Sure. I will use the PME henceforth. Are the other parameters okay in the
>> .mdp file?
>
> I made several comments, embedded within the .mdp te
On 7/13/16 9:12 AM, Deep Bhattacharya wrote:
Sure. I will use the PME henceforth. Are the other parameters okay in the .mdp
file?
I made several comments, embedded within the .mdp text. Correct all of them
carefully.
-Justin
Sent from my iPhone
On Jul 13, 2016, at 8:09 AM, Justin
Sure. I will use the PME henceforth. Are the other parameters okay in the .mdp
file?
Sent from my iPhone
> On Jul 13, 2016, at 8:09 AM, Justin Lemkul wrote:
>
>
>
>> On 7/13/16 9:07 AM, Deep Bhattacharya wrote:
>> Hello Justin,
>> Is it appropriate to use Nose-Hoover thermostat with Parrin
On 7/13/16 9:07 AM, Deep Bhattacharya wrote:
Hello Justin,
Is it appropriate to use Nose-Hoover thermostat with Parrinello rahman
thermostat in the .mdp file? In the previous mail I have reduced the time step
, will all there changes be appropriate for the simulation ?
It's fine as long as
Hello Justin,
Is it appropriate to use Nose-Hoover thermostat with Parrinello rahman
thermostat in the .mdp file? In the previous mail I have reduced the time step
, will all there changes be appropriate for the simulation ?
Sincerely,
Deep
Sent from my iPhone
> On Jul 13, 2016, at 8:01 AM, Jus
Sent from my iPhone
> On Jul 13, 2016, at 8:01 AM, Justin Lemkul wrote:
>
>
>
>> On 7/13/16 8:56 AM, Deep Bhattacharya wrote:
>> Hello Tsjerk,
>>
>> These are the notes that I got before running the NPT equilibration
>>
>>
>> NOTE 1 [file npt.mdp]:
>> leapfrog does not yet support Nose-H
On 7/13/16 8:56 AM, Deep Bhattacharya wrote:
Hello Tsjerk,
These are the notes that I got before running the NPT equilibration
NOTE 1 [file npt.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
Generated 165 of the 1596 non-bonded parameter combinations
Excl
Hello Tsjerk,
These are the notes that I got before running the NPT equilibration
NOTE 1 [file npt.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_
Hi Deep,
What force field? What system? How many cores? Did you try running on one?
What error? Did pdb2gmx or grompp give any warnings?
Cheers,
Tsjerk
On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya
wrote:
> Hello,
> My system is blowing up for the protein carbohydrate solvent complex. I
Hello,
My system is blowing up for the protein carbohydrate solvent complex. I
have attached the mdp file below. The NPT and NVT were in good accordance
to tutorial listed by Justin. 'Please help me solve the issue.
title = CD44 complex MD simulation
; Run parameters
integrator = md
On 12/16/15 12:54 PM, NISHA Prakash wrote:
Dear Justin,
You are right and I totally agree with you. But, the point that I was
trying to make was that "the same input coordinates and input .mdp files
run in 4.5.4 and fail in 5.0.5". Also, if this situation persists, does
that mean the results
Dear Justin,
You are right and I totally agree with you. But, the point that I was
trying to make was that "the same input coordinates and input .mdp files
run in 4.5.4 and fail in 5.0.5". Also, if this situation persists, does
that mean the results that have been obtained from the version 4.5.4
On 12/16/15 12:08 AM, NISHA Prakash wrote:
Dear Justin,
I am simulating a protein ligand complex. The protein co-ordinate file that
I have taken is an output of the simulation of the protein alone in
Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still
facing this problem whe
Dear Justin,
I am simulating a protein ligand complex. The protein co-ordinate file that
I have taken is an output of the simulation of the protein alone in
Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still
facing this problem wherein I get the LINCS warning for only the prote
On 12/15/15 8:42 AM, NISHA Prakash wrote:
Hi all,
I am trying to simulate a protein using similar parameters as in the
tutorial - Protein ligand by Justin Lemkul.
I am facing a problem wherein the protein simulation is exploding only in
this version - Gromacs-v5.0.5 but not in the older versi
Hi all,
I am trying to simulate a protein using similar parameters as in the
tutorial - Protein ligand by Justin Lemkul.
I am facing a problem wherein the protein simulation is exploding only in
this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4.
The warning message is as
Hi,
That's indeed curious. Please open an issue at http://redmine.gromacs.org and
attach your .tpr and .cpt files so we can see if we can reproduce it.
Mark
On Wed, Dec 2, 2015 at 9:22 PM Marlon Sidore
wrote:
> It actually went on a few steps before blowing up, it didn't blow up
> directly at
It actually went on a few steps before blowing up, it didn't blow up
directly at restart.
Does that mean it simply blew up because of the system ? It always blows up
a little time after restarting though, and that's strange given the time it
ran the first time.
gmx dump doesn't say anything specia
Hi,
That should work, and I can't see why it should ever blow up. What does gmx
dump have to say about vict.cpt? Does the restarted .log file say after the
restart?
Mark
On Wed, Dec 2, 2015 at 8:20 PM Marlon wrote:
> Hello,
>
> I have a problem continuing my simulation after the queue system s
Hello,
I have a problem continuing my simulation after the queue system stops
the job (as I can't get -maxh to work). I would like to append the files
to the old ones.
The first production run, which ran one full day and 155 million steps,
had the mdrun options:
mdrun_mpi -deffnm vict -cpi equil.
Hi Carlos,
You can try to contact Floris about the MGDG model.
Cheers,
Tsjerk
On Fri, Mar 6, 2015 at 9:56 PM, Carlos Navarro Retamal
wrote:
> Hi Tsjerk,
> I tried to follow as closer as i could the parameters you used, but again
> without luck:
> .mdp file:
> dt = 0.01
> nsteps
Hi Tsjerk,
I tried to follow as closer as i could the parameters you used, but again
without luck:
.mdp file:
dt = 0.01
nsteps = 500
nstxout = 0
nstvout = 0
nstlog = 1
nstxtcout= 1000
xtc-precision= 10
rlist
Hi Carlos,
Most of that work (and the tutorials) was started some time ago. You can
use Gromacs 5. At some point, the tutorials will get updated, but usually
if there's pressure from a course or workshop. Otherwise the science comes
first :)
Cheers,
Tsjerk
On Mar 6, 2015 8:38 PM, "Carlos Navarro
Hi Tsjerk,
Thanks for your kind reply. I just start to reading your manuscript and notice
that you used GROMACS version 4.5.5 instead of the latest one (5.X)
Is there an specific reason to do these? (maybe martini works in a better way
with older version of gromacs? )
I’m asking you these, becaus
Hi Carlos,
Other things to consider are doing a first short equilibration on a single
processor and increasing the dom.dec. radius to 1.6 or 1.8 (mdrun -rdd
1.6). Maybe you might want to check the just accepted manuscript on
thylakoid membranes from the Martini group (
http://dx.doi.org/10.1016/j.
Dear Justin,
I was looking into the paper where the ‘martini’ group described the parameters
for glycolipids, and the mention that in order to equilibrate some glycolipids
the had to used a timestep of 5fs. Sadly they not mention which glycolipid
were, so i reduced the timestep from 20fs to 10fs
Dear Justin,
Thanks for your kind reply.
Is there a way to set up a bilayer membrane system without a protein using
insane? I’ve already several CG simulations with this protein, so i'm pretty
sure that its parameters are ok. I do have some issues with the glycolipid used
(MGDG) This is the firs
On 3/6/15 8:15 AM, Carlos Navarro Retamal wrote:
Dear Gromacs users,
I'm trying to perform a CG simulations of a system consisting in a protein
locate at 5 nm with respect to the charged groups of a MGDG membrane.
I first performed an EM in vaccum.
After that, to constructed the system i use i
Dear Gromacs users,
I'm trying to perform a CG simulations of a system consisting in a protein
locate at 5 nm with respect to the charged groups of a MGDG membrane.
I first performed an EM in vaccum.
After that, to constructed the system i use insane.py as following:
./insane.py -f minimization-va
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