Re: [gmx-users] Equilibration Problem.

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

[gmx-users] Equilibration Problem.

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

[gmx-users] Equilibration Error, Skew Factor

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

Re: [gmx-users] Equilibration step not moving forward

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 >

[gmx-users] Equilibration step not moving forward

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

Re: [gmx-users] equilibration error

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?

[gmx-users] equilibration error

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

[gmx-users] Equilibration step in MD

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

Re: [gmx-users] Equilibration

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

Re: [gmx-users] Equilibration

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

Re: [gmx-users] Equilibration

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

Re: [gmx-users] Equilibration

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

[gmx-users] Equilibration

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-

Re: [gmx-users] Equilibration

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

Re: [gmx-users] Equilibration

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

[gmx-users] Equilibration

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

Re: [gmx-users] Equilibration using position restraints in NPT

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

Re: [gmx-users] Equilibration using position restraints in NPT

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 <n.gandh...@gmail.com> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Equilibration using po

Re: [gmx-users] Equilibration using position restraints in NPT

? Message: 1 Date: Sun, 8 Oct 2017 23:38:58 +1000 From: Neha Gandhi <n.gandh...@gmail.com> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Equilibration using position restraints in NPT Message-ID: <CA+Hq8HyXsHSXfNAe5AmBmy3ArxS-=aZHJckdJSC4yqWUMJDbmA@mail.

[gmx-users] Equilibration using position restraints in NPT

rom: Neha Gandhi <n.gandh...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Equilibration using position restraints in NPT > Message-ID: > <CA+Hq8HyXsHSXfNAe5AmBmy3ArxS-=aZHJckdJSC4yqWUMJDbmA@mail. > gmail.com> > C

Re: [gmx-users] Equilibration using position restraints in NPT

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

[gmx-users] Equilibration using position restraints in NPT

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

Re: [gmx-users] Equilibration at each temperature in simmulated annealing

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.

Re: [gmx-users] Equilibration at each temperature in simmulated annealing

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

[gmx-users] Equilibration at each temperature in simmulated annealing

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

Re: [gmx-users] Equilibration

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

[gmx-users] Equilibration

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

Re: [gmx-users] Equilibration of Lipid Bilayers created through charmm-gui

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

[gmx-users] Equilibration of Lipid Bilayers created through charmm-gui

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

Re: [gmx-users] equilibration

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 )

[gmx-users] equilibration

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

Re: [gmx-users] Equilibration

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

Re: [gmx-users] Equilibration

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

Re: [gmx-users] Equilibration

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 (

[gmx-users] Equilibration

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

[gmx-users] Equilibration

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

[gmx-users] EQUILIBRATION

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

[gmx-users] equilibration and production run

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

Re: [gmx-users] Equilibration problem

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

[gmx-users] Equilibration problem

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

[gmx-users] Equilibration error

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

Re: [gmx-users] Equilibration error

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

Re: [gmx-users] Equilibration fails only when run from script

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

[gmx-users] Equilibration fails only when run from script

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

Re: [gmx-users] Equilibration from Non-shifted to Shifted Potential

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