On 1/7/20 6:35 PM, Neena Susan Eappen wrote:
Hi Justin,
Thank you for your answer. I haven't written scripts before, so I was wondering
is there a sample script I can see for looping in gromacs.
What you're trying to do is similar to the logic in
http://www.mdtutorials.com/gmx/membrane_pr
users@maillist.sys.kth.se
Subject: Re: [gmx-users] Simulated Annealing command line
Hi Kenny,
Thank you for your answer, but I did not understand clearly. For say 30 cycles
of simulated annealing, what I have been doing currently is going through the
following steps ( equilibration, annealing, produ
January 5, 2020 8:43 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Simulated Annealing command line
Hello gromacs users,
For simulated annealing, I want to repeat cycle (equilibration, annealing,
production run, energy minimization) say n times with the energy minimized
s
appreciated,
Thank you,
Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
From: Neena Susan Eappen
Sent: Sunday, January 5, 2020 8:43 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Simulated Ann
: zondag 5 januari 2020 21:43
Aan: gromacs.org_gmx-users@maillist.sys.kth.se
Onderwerp: [gmx-users] Simulated Annealing command line
Hello gromacs users,
For simulated annealing, I want to repeat cycle (equilibration, annealing,
production run, energy minimization) say n times with the energy
Hello gromacs users,
For simulated annealing, I want to repeat cycle (equilibration, annealing,
production run, energy minimization) say n times with the energy minimized
structure from end of cycle 1 to be used as starting structure for cycle 2. I
was wondering is there a way to do this as a l
Hello Neena,
The outline you give appears reasonable for exploring peptide conformations. It is very hard to judge appropriateness
though without knowing what you are trying to learn from your system.
The unspecified position restraints might defeat the purpose of the simulated annealing if y
Hello gromacs users,
My goal is to do a better conformational sampling of my peptides using
simulated annealing. Is my following procedure correct?
1- Energy minimization
2- NVT equilibration with position restraints say at 600 K for 100 ps
3- Simulated annealing with position restraints to cool
Hello gromacs users,
My goal is to do a better conformational sampling of my peptides in vacuum. I
was wondering do I simulated annealing with position restraints or not?
Many thanks,
Neena
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Hi GMX users,
I am running an annealing simulation with version 2019, I found that once I
have the annealing section in my .mdp file. The temperature coupling
information is not recognized and written into the mdout.mdp. And my
simulated annealing process was kept at 0 K through the whole time. On
Use the final configuration to start a new annealing calculation. As there
is no real ensemble to preserve, there is nothing to manage.
Mark
On Sat., 9 Feb. 2019, 10:48 Shan Jayasinghe,
wrote:
> Dear Gromacs Users,
>
> How do we extend a simulated annealing?
>
> Thank you.
>
> Best Regards
> Sh
Dear Gromacs Users,
How do we extend a simulated annealing?
Thank you.
Best Regards
Shan Jayasinghe
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Dear Prof. Justin,
Thank you very much for the answer. It is really helpful.
On Tue, Feb 5, 2019 at 1:48 AM Justin Lemkul wrote:
>
>
> On 2/1/19 4:45 PM, Shan Jayasinghe wrote:
> > Dear Gromacs Users,
> >
> > I did a simulated annealing for my system and now I want to analyse my
> > data. Can a
On 2/1/19 4:45 PM, Shan Jayasinghe wrote:
Dear Gromacs Users,
I did a simulated annealing for my system and now I want to analyse my
data. Can anyone suggest me a tutorial for this? What type of information
we can get from simulated annealing?
Usually annealing is just applied during equili
Dear Gromacs Users,
I did a simulated annealing for my system and now I want to analyse my
data. Can anyone suggest me a tutorial for this? What type of information
we can get from simulated annealing?
I want to know whether the generated .gro file corresponds to the last
temperature we defined i
sion list for GROMACS users
Sent: Monday, February 19, 2018 8:33 PM
Subject: Re: [gmx-users] simulated annealing
On 2/19/18 2:31 PM, Ahmed Mashaly wrote:
Thanks, Justin.
I had set it to 300K before (as the original mdp was), but now I found others
with 0
Now when if we look at the log
So I redo the NVT with ref-t and gen-temp set to zero or I neglect this issue?
Kind Regards,Ahmed
From: Justin Lemkul
To: Discussion list for GROMACS users
Sent: Monday, February 19, 2018 8:33 PM
Subject: Re: [gmx-users] simulated annealing
On 2/19/18 2:31 PM, Ahmed Mashaly
On 2/19/18 2:31 PM, Ahmed Mashaly wrote:
Thanks, Justin.
I had set it to 300K before (as the original mdp was), but now I found others
with 0
Now when if we look at the log file, you can see ref temp for both groups
starts from 0 and increasing, but the temperature in the details goes from
On 2/19/18 2:06 PM, Ahmed Mashaly wrote:
Hi
If I want to heat the system from 0 to 300K gradually in NVT via simulated
annealing
the ref-t and gen-temp should be 0 or 300?
Both are irrelevant. ref-t is ignored when using simulated annealing,
because the reference value changes over time. If
Hi
If I want to heat the system from 0 to 300K gradually in NVT via simulated
annealing
the ref-t and gen-temp should be 0 or 300?
Kind Regards,Ahmed
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Dear gromacs users,
I am extremely sorry for my previous incomplete mail. By mistaken I have
pressed some short cut key.
I have one peptide which has 25 residues. I have done simulation for 100ns.
When I presented my analysis in lab, I was suggested to do investigation of
my simulation by simul
Hi,
Simulated annealing for system preparation is a waste of time in my
opinion. Recommended simulation preparation protocols are on the Gromacs
website, and are all you need unless your starting conformation has serious
problems, and then simulated annealing may or may not help
Mark
On Wed, 31
Hi all,
I am using Gromacs version 4.5.6 for peptide simulation. The
structure of the peptide (16mer) was predicted from Pepfold3 server. I did
Simulated annealing so that the side chains get properly oriented and the
predicted structure will reach its global optimum so that the structure
be
On 4/8/16 9:21 AM, xy21hb wrote:
Dear all,
I would like to get a gel phase of a lipid bilayer system by simulated
annealing (SA).
I wonder in which step (NVT equilibration/velocity-generation, NPT
equilibration, or MD run) I should apply SA.
Run the SA under whatever ensemble you wish to
Dear all,
I would like to get a gel phase of a lipid bilayer system by simulated
annealing (SA).
I wonder in which step (NVT equilibration/velocity-generation, NPT
equilibration, or MD run) I should apply SA.
Best,
Yao
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On 11/16/13 8:14 PM, Raghunath Satpathy wrote:
is it necessary to heat and cool protein in simulated annealing ? i wanna to
check thermostability by md simulation only by increasing temp (without cooling
) in many picoseconds , is it possible to get go
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