Dear Gromacs users,
I tried to do the simulation of a single molecule in cyclohexane, I'm using
gromos 53a6 force field for both molecules.
i did all the minimization steps. After npt, I runned for 25 000 000 steps.
just after around 100 000 steps, the system stops and i got this fatal
error:
Fa
.
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Za Pour
> Sent: Wednesday, 8 May 2013 4:58 AM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] equilibration of the simulated systems
>
> Dear gmx users
> wou
yes.
you can use g_energy to plot what you need (T, density or whatever) and
decide if it is acceptable or not.
In the latter case you simply have to extend your run (see
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations)
cheers
Francesco
On Tue, 7 May 2013, at 06:58 PM, Za Pou
Dear gmx users
would you please tell me how I can be sure that my simulation time is long
enough? is it appropriate way to use g_energy program and calculate total
energy ?
thank you
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On 9/19/12 12:27 PM, Lara Bunte wrote:
Hello
I want to equilibrate water around the amino acid alanin. I guess I have no
further errors up to here.
In my pdb file of alanin stands in the first line COMPND Alanin
In my topology in the [ moleculetype ] block stands at name:
Protein_chain_A. A
Hello
I want to equilibrate water around the amino acid alanin. I guess I have no
further errors up to here.
In my pdb file of alanin stands in the first line COMPND Alanin
In my topology in the [ moleculetype ] block stands at name:
Protein_chain_A. At the end of the topology file stands in
Hi all,
Can you please guide me how one can calculate fraction of gauche+ and
gauche- defects in the center of a polymer chain?
Appreciate you help.
Juliete
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On 15/09/2011 5:13 AM, Juliette N. wrote:
Hello,
For the equilibration one usually looks at the total energy or the
observable of interest to be independent of time. I wanted to figure
out when we are referring to equilibration which of the run time or
n_steps parameters are important. One co
Juliette N. wrote:
Hello,
For the equilibration one usually looks at the total energy or the
observable of interest to be independent of time. I wanted to figure out
when we are referring to equilibration which of the run time or n_steps
parameters are important. One could run 1,000,000 ste
Hello,
For the equilibration one usually looks at the total energy or the
observable of interest to be independent of time. I wanted to figure out
when we are referring to equilibration which of the run time or n_steps
parameters are important. One could run 1,000,000 steps with dt of 0.001 ps
or
bharat gupta wrote:
Hi,
I carried out the equilibration step using the npt file given in teh
lysozyme tutorial... I have generated the graph for both pressure and
density .. I want to know how to analyse such graph ... If the graph
fluctuates between certain range of values like the one gi
Hi,
I carried out the equilibration step using the npt file given in teh
lysozyme tutorial... I have generated the graph for both pressure and
density .. I want to know how to analyse such graph ... If the graph
fluctuates between certain range of values like the one given in the
lysozyme tutorial
Thanks Justin. I got it now.
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Wednesday, October 13, 2010 12:07 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Equilibration of POPC - Lipid
NG HUI WEN wrote:
Dear gmxusers,
I have obtained a box of POPC with a starting dimension of 12.48, 12.36,
and 6.92 (nm) using genconf –nbox 2 2 1. The original lipid was
downloaded from Prof. Tieleman’s site (popc128a.pdb).
My intention is to equilibrate the new bilayer such that t
Dear gmxusers,
I have obtained a box of POPC with a starting dimension of 12.48, 12.36, and
6.92 (nm) using genconf -nbox 2 2 1. The original lipid was downloaded from
Prof. Tieleman's site (popc128a.pdb).
My intention is to equilibrate the new bilayer such that the lipids,
particularl
Nilesh Dhumal wrote:
I am using the opls parameters from Lope's paper.
In vaccum energy minimzatin is working well. MD is not at all working.
My other systems are running well. In the present system I changed the
anion, cation parameters are fine.
Is the problem with anion parameters?
If it
I am using the opls parameters from Lope's paper.
In vaccum energy minimzatin is working well. MD is not at all working.
My other systems are running well. In the present system I changed the
anion, cation parameters are fine.
Is the problem with anion parameters?
Nilesh
On Fri, June 4, 2010 10:
Nilesh Dhumal wrote:
Hello,
I am trying to equilibrate my system, ionic liquids. My simulations gets
stop immediately. I reduced the step size. I modified initial structure.
I changed the box size. I checked force field parameters. I am using
opls foce field. I repeated my energy minimizati
Hello,
I am trying to equilibrate my system, ionic liquids. My simulations gets
stop immediately. I reduced the step size. I modified initial structure.
I changed the box size. I checked force field parameters. I am using
opls foce field. I repeated my energy minimization 2-3 times. I could not
Emanuel Peter wrote:
Dear Gromacs users,
I have read about an equilibration procedure for proteins.
It has the following sequence:
- cool down to 20 K an let this run for about 1 ps.
- heat the system up with 10 K every 500 steps until you get 300 K.
- do a run for 4 ps at 300 K.
Is this kin
Dear Gromacs users,
I have read about an equilibration procedure for proteins.
It has the following sequence:
- cool down to 20 K an let this run for about 1 ps.
- heat the system up with 10 K every 500 steps until you get 300 K.
- do a run for 4 ps at 300 K.
Is this kind of equilibration really
Arnab Senapati wrote:
Hi,
Can anyone please tell me How to remove the equilibration time from
calculating averages.
Start by looking at the commmand line options for the tools you're
using, e.g. -b. Otherwise, your question is too general to get a
specific answer.
Mark
_
Hi,
Can anyone please tell me How to remove the equilibration time from
calculating averages.
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Hi Lal,
Well, if you set the number of steps to 0, it should get you rid of any errors.
But for the rest, the LINCS errors don't have to do with the length of
the simulation but with what's in there.You can try and decrease the
time step as is suggested by the program. But the LINCS error is
likel
Dear gromacs experts,
I have decrease the timesteps from 50,000 to 10,000 but still the error of
LINCS comes.where should I do correction?
regards,
Lal badshah/
SYED LAL BADSHAH
M.Phil Scholar
NCE in Physical Chemistry,
University of Peshawar.
NWFP,Pakistan.
Cell # 03349060632.
Send instan
> Dear experts,
> Hi,I am doing equilibration ,it crashes a few times due to power
> breakdown.Now I started again witj the following commands and the
> following output comes.what should i do?
Like it says, your simulation box is badly broken. That means your input
is broken somehow. Pay attenti
Dear experts,
Hi,I am doing equilibration ,it crashes a few times due to power breakdown.Now
I started again witj the following commands and the following output
comes.what should i do?
please guide me
grompp -f eq.mdp -c em.pdb -p topol.top -o eq.tpr
nohup mdrun -s eq.tpr -o eq.trr-c eq_b4md.gr
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