Did you visualise the system? What would you expect the density of the
system to be?
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
---
Hello Everyone!
Trying to simulate a system build in PACKMOL having peptides, water and
small molecules. Energy minimization and other process for setting up md
simulation went fine.
NVT AND NPT FOR 1000PS BUT system didn't Equilibrated.
Average required temperature maintained.
*Energy
Hello,
I am working on a coarse-grained polymer system having various chain length
(20 & 62), dissolved in water with different counter-ion concentrations.
While equilibrating the systems I am consistently facing an error.
For chain Length 20;
Fatal error:
The X-size of the box (6.716921) times t
Hi,
We can't help you unless you're more specific. What error is occurring?
Kevin
On Tue, Feb 5, 2019 at 1:30 AM Deepanshi wrote:
> Hello,
> I am trying to equilibrate a bilayer vesicle which I have prepared using
> martini maker of charmm-GUI. The vesicle is made up of POPC and has around
> 3
Hello,
I am trying to equilibrate a bilayer vesicle which I have prepared using
martini maker of charmm-GUI. The vesicle is made up of POPC and has around
3000 lipids. I am trying to equilibrate the system but steps are not
moving forward and I am stuck at this point. Here are the details of the
.m
What is actually different in the mdp file between each of these
steps? What about the cluster run on, or mdrun command used for each
of the steps?
How have you determined that each step in the process is long enough
i.e. what are you looking at to see if things have stabilised
sufficiently?
The
Hello,
I am planing to do MD of a membrane protein bound to a ligand.
I already have my files and I am doing my 6 step equilibration with
reducing force constants.
However, in the 5th step, it gave an error saying that the previous system
(4th step) was not well equilibrated:
Fatal error:
5 partic
Dear all,
The rmsd obtained after equilibration of protein-protein complex at 1atm
pressure is quite high(5times) but the rmsd obtained for only 100ps
simulatrion of equilibration is quite stable. Which rmsd should be
considered?
--
Best regards,
*Shyantani Maiti*
--
Gromacs Users mailing list
On 2/28/18 6:38 AM, Amin Rouy wrote:
Thanks Justin, however,
I run a simulation of a solute in water. I have 2 question please:
1- After NVT equilibrium, I see that all quantities like
energies and
temperature become stable, except pressure. Should I continue
Thanks Justin, however,
>
>> I run a simulation of a solute in water. I have 2 question please:
>>
>> 1- After NVT equilibrium, I see that all quantities like energies and
>> temperature become stable, except pressure. Should I continue till
>> pressure
>> also goes stable? or can I move forward a
sorry but I did not get my answer.
In NVT equilibration, the pressure is not equilibrated yet, can I move
forward to production run? (I see that I have no blow up when I run
production)
On Wed, Feb 28, 2018 at 10:38 AM, Quyen V. Vu wrote:
> No matter how many steps of equilibration you want to r
No matter how many steps of equilibration you want to run.
You need to run production run when your configuration is reasonable and in
which condition, which ensemble you want to mimic
On Wed, Feb 28, 2018 at 3:54 PM, Amin Rouy wrote:
> Hi,
>
>
> I run a simulation of a solute in water. I have 2
Hi,
I run a simulation of a solute in water. I have 2 questions please:
1- After NVT equilibrium, I see that all quantities like energies and
temperature become stable, except pressure. Should I continue untill
pressure becomes stable too? or can I move forward and do it in
production run?
2-
Not sure about with constant volume, as I don't tend to run under
those conditions, but with constant pressure the pressure will always
fluctuate quite substantially.
How big the fluctuation is depends on the size of the system, the
later the system is, the smaller the fluctuations.
Small system
On 2/27/18 10:05 AM, Amin Rouy wrote:
Hi,
I run a simulation of a solute in water. I have 2 question please:
1- After NVT equilibrium, I see that all quantities like energies and
temperature become stable, except pressure. Should I continue till pressure
also goes stable? or can I move forwar
Hi,
I run a simulation of a solute in water. I have 2 question please:
1- After NVT equilibrium, I see that all quantities like energies and
temperature become stable, except pressure. Should I continue till pressure
also goes stable? or can I move forward and do it in production run?
2- My inte
On Sun, Oct 8, 2017 at 11:30 PM Neha Gandhi wrote:
> Thank you Mark.
>
> The nanotube is 2x2x13 nm long. Then I use editconf with -c and -d 2 and
> solvate using spc216.gro.
>
Please visualize that result. Such a command would put solvent all around
your nanotube, so it could not have an infin
can I calculate box size after NVT so that I get density of 1 or
0.99
when using pressure coupling?
Message: 1
Date: Sun, 8 Oct 2017 23:38:58 +1000
From: Neha Gandhi
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Equilibration using position restraints in NPT
Message-ID
?
Message: 1
Date: Sun, 8 Oct 2017 23:38:58 +1000
From: Neha Gandhi
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Equilibration using position restraints in NPT
Message-ID:
Content-Type: text/plain; charset="UTF-8"
This is a very common post on previous ma
rom: Neha Gandhi
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Equilibration using position restraints in NPT
> Message-ID:
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> This is a very common post on previous mailing lis
Hi,
The simplest explanation is that your box size is inappropriate for the
contents. If the box wants to change size but the nanotube is restrained to
fixed positions then you have an invalid model.
Mark
On Sun, 8 Oct 2017 15:39 Neha Gandhi wrote:
> This is a very common post on previous mail
This is a very common post on previous mailing list however, I am still not
able to fix the problem of position restraints during NPT.
I have a carbon nanotube aligned to z-direction. I am trying to simulate
infinite nanotube using periodic conditions. It is common to use position
restraints for n
Hi,
That's still not going to have any effect. You're probably referring to
ref-t, which is exactly what simulated annealing is documented to replace.
Mark
On Tue, Sep 26, 2017 at 3:15 PM lan hoa Trinh wrote:
> Thanks! sorry for the spelling error, I just meant tcoupl.
>
> Sent from my iPhone
Thanks! sorry for the spelling error, I just meant tcoupl.
Sent from my iPhone
> On Sep 26, 2017, at 6:30 AM, Mark Abraham wrote:
>
> Hi,
>
> It'll equilibrate if you leave it alone long enough at an annealing point,
> as normal. See
> http://manual.gromacs.org/documentation/2016.4/user-guide/
Hi,
It'll equilibrate if you leave it alone long enough at an annealing point,
as normal. See
http://manual.gromacs.org/documentation/2016.4/user-guide/mdp-options.html#simulated-annealing.
I don't know what you mean by referring to the non-existent t_couple
Mark
On Tue, Sep 26, 2017 at 8:49 AM
Hi all,
I would like to cool my system from 200K to 100K via multiple intermediate
temperatures and at each temperature, the system is equilibrated for a
while before decreasing temperature.
I am thinking of doing something like this:
annealing_temp = 200 150 150 100 100
But I am afraid this is not
That ultimately depends on what physical property you are hoping to
show is at "equilibrium". For example, see
https://twitter.com/dr_dbw/status/907735156382777344 for how
temperature, total energy, volume, density and pressure change with
time for an example system. Pressure and temperature you
Dear users,
I need to demonstrate that my box is in equilibrium. What is the maximum
slope of the energy or the volume in function of time to demosntrate it? .
Or exist anothe parameter to follow. Thank you very much.
--
*Dr. Álvaro Ruiz *
*Physicochemical Molecular LaboratoryDepartamento
On 7/17/17 2:14 PM, Nidhin Thomas wrote:
Hello everyone,
I have created an 'alpha-helix protein embedded in a lipid bilayer’ system
using charmm-gui.
I used the mdp files provided by charmm-gui directly without changing the
number of steps or constraints for equilibration. I ran final simu
Hello everyone,
I have created an 'alpha-helix protein embedded in a lipid bilayer’ system
using charmm-gui.
I used the mdp files provided by charmm-gui directly without changing the
number of steps or constraints for equilibration. I ran final simulation for
200 ns without any constraints an
On 7/14/17 7:43 AM, farial tavakoli wrote:
Hi justin
Thank you for reply and sorry for sending in another email, because when i wanted to reply, it was rejected.Actually, since i am a new gromacs user, i used all .mdp files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tu
Hi justin
Thank you for reply and sorry for sending in another email, because when i
wanted to reply, it was rejected.Actually, since i am a new gromacs user, i
used all .mdp files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym
4 ) tuturial in gromacs. And did all the steps and issu
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Hi justin
Thank you for replyActually, since i am a new gromacs user, i used all .mdp
files ( em.mdp, nvt.mdp,...) in protein-l
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; }Hi justin
Thank you for replyActually, since i am a new gromacs user, i used all .mdp
files ( em.mdp, nvt.mdp,...) in protein
On 7/13/17 11:21 AM, farial tavakoli wrote:
Hi Justin
Thank you so much for your reply about minimize ligand in vacuoaccording to
:http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
I minimized my protein and ligand alone to fix the problem ( LINCS
Hi Justin
Thank you so much for your reply about minimize ligand in vacuoaccording to
:http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
I minimized my protein and ligand alone to fix the problem ( LINCS warning, (
one or more water molecules can not to b
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } HiI am a new GROMACS user and i am trying to run a
simulation on 4LY1 protein and my designed drug to check their interactio
HiI am a new GROMACS user and trying to run md on HDAC2 with PDB ID: 4LY1. but
when I wanted to performance equilibration , i got this ERROR:
step 1: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if
a
Hi gromacs users,
I intend to do the following steps for protein ligand simulations (for
linear interaction energy)
(1) Energy minimization
(2) NVT equilibration (with restraints on protein and ligand)
(3) NPT equilibration (with restraints on protein and ligand)
(4) NPT production
During NVT
On 8/4/16 6:09 AM, amitbe...@chemeng.iisc.ernet.in wrote:
Hello everyone,
I prepared a bilayer using PACKMOL. Then ran energy minimisation. Till
this point the structure completely intact. Then I ran nvt on the
structure. At this point GROMACS-5.1.2 is giving back more than one pdb
files (named
Hello everyone,
I prepared a bilayer using PACKMOL. Then ran energy minimisation. Till
this point the structure completely intact. Then I ran nvt on the
structure. At this point GROMACS-5.1.2 is giving back more than one pdb
files (named step**.pdb) instead of usual .gro file.
Does anyone know how
On 2/8/16 5:22 AM, Abid Channa wrote:
Hi gromacs users,
I have found error in equalibration step in my simulation. Kindly give your
valuable suggestions.
Fatal error:
2 particles communicated to PME rank 5 are more than 2/3 times the cut-off out
of the domain decomposition cell of their cha
Hi gromacs users,
I have found error in equalibration step in my simulation. Kindly give your
valuable suggestions.
Fatal error:
2 particles communicated to PME rank 5 are more than 2/3 times the cut-off out
of the domain decomposition cell of their charge group in dimension x.
This usually mea
On 12/1/15 6:39 AM, R Corey wrote:
Hello
I am running a series of FEP MD simulations using Gromacs 5.0.4, for each a
steepest descents minimization, NVT equil, NPT equil and production run,
all controlled by a central script. However, only about 50% of the runs get
through the NVT equilibratio
Hello
I am running a series of FEP MD simulations using Gromacs 5.0.4, for each a
steepest descents minimization, NVT equil, NPT equil and production run,
all controlled by a central script. However, only about 50% of the runs get
through the NVT equilibration without crashing - crash error as bel
ewald_rtol affects PME.
http://comments.gmane.org/gmane.science.biology.gromacs.user/50202
On Fri, Nov 14, 2014 at 10:39 AM, Johnny Lu wrote:
> In another mdp file, i specified "vdw-modifier=Potential-shift-Verlet",
> and then in the log file, I see the same line "vdw-modifier =
> Potential-shi
In another mdp file, i specified "vdw-modifier=Potential-shift-Verlet", and
then in the log file, I see the same line "vdw-modifier = Potential-shift",
and I use "cutoff-scheme = Verlet" in all of my simulations.
Since i use rlist=1.3, and verlet-buffer-drift=-1. I guess the line
"vdw-modifier=Pot
On Fri, Nov 14, 2014 at 3:51 PM, Johnny Lu wrote:
> I guess I get the idea now. F = -dV(x)/dx. So no time derivative is
> involved. So shifting the potential would not cause a suddenly impulse on
> the system.
>
> By the way, is Potential-shift the default vdw and coulomb-modifier (so
> that is u
I guess I get the idea now. F = -dV(x)/dx. So no time derivative is
involved. So shifting the potential would not cause a suddenly impulse on
the system.
By the way, is Potential-shift the default vdw and coulomb-modifier (so
that is used even if i didn't specify a modifier) for gromacs 4.6.7?
I d
Hi,
Try it and see ;-)
mdrun -nsteps 10 -reprod -deffnm shifted
mdrun -nsteps 10 -reprod -deffnm not-shifted
gmx check -f shifted -f2 not-shifted
gmx check -e shifted -e2 not-shifted
Alternatively, given that the forces are not computed from the energies
(e.g. by central difference or some such)
Hi.
If I change my potential from non-shifted to shift, will the sudden change
of energy from non-shifted to shifted potential at step 0 completely mess
up the equilibration?
Thanks again.
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