Hi Justin
Thank you very much for your prompt reply!
I have used GROMACS96 force field to simulate pure coal density. It perfectly
matches the real coal density.
Now I want to apply this coal model to investigate gas adsorption in coal. But
I do not think GROMACS can do this. Therefore, I am
Dear list,
I am trying to use MTTK barostat in GROMACS 4.5.5.
After analyzing the result for a while, I found that the conserved energy (not
total energy) of MTTK is drifting during the simulation.
The .xvg, .edr files are uploaded at [1] and [2]. It is drifting with a
constant ratio of ca. -185
Won't this same stochastic nature of MD provide for different,
independent trajectories even if restarted from a previous, equilibrated
frame even without resetting velocities, i.e., as a continuation run
using the velocities recorded in the gro file of the selected snapshot?
Felipe
On 11/22/
Stochastic and chaotic are not identical. Chaotic means that differences in the
initial state will grow exponentially over time.
Erik
22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD:
> Won't this same stochastic nature of MD provide for different, independent
> trajectories even if restarted fr
Would "non-deterministic" be correct to characterize the nature of MD as
well? There is also deterministic chaos ... And what about the outcome
of starting several trajectories from the same equilibrated frame as
continuation runs, i.e., using its velocities? Could they be considered
independen
U r right FLorian
I have also tried playing around the tau_p but in vain.
Even in absence of any constraints, it is giving almost same result.
Em thinking to move again to Leap-Frog, NH , PR. I see people
generally use this combination a lot.
Thanks
Tarak
On Wed, Nov 21, 2012 at 8:08 PM, Florian
> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] Im Auftrag von tarak karmakar
> Gesendet: Donnerstag, 22. November 2012 10:15
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] pressure_coupling
>
> U r right FLoria
It will depend on the integration algorithms, parallelization, etc. The
equations are deterministic, but numerical differences may arise e.g. from
different ordering of floating point numbers being added together in different
simulations. The chaotic nature of MD would then have the simulations
Not to forget about the additional stochastic term in the V-rescale
thermostat, when it's used. Since the equations are evidently
deterministic, is the chaotic nature of MD just a numerical effect?
The practical point: if the velocities are reset upon a restart from an
equilibrated frame in or
Hi,
It seems that the one directional diffusion constants can be obtained by
means of g_msd ...blabla...-type z.
However, my question is that I don't want to obtain the diffusion constants.
Actually, the MSD trajectory file for all 3 dimensional data can be
obtained by conventional g_msd...
Inst
MD is chaotic regardless of how differences, however small, are created in the
first place. This was just one example.
Stochastic terms in e.g. the v-rescale thermostat will rely on the same
sequence of random numbers in separate simulations if the random number
generator is seeded in the same
On 11/21/2012 06:02 PM, Ali Alizadeh wrote:
1- In your opinion, Can i simulate that system?
In my (humble) opinion:
1)Of course you can simulate that system...however I doubt that, without
starting from the exact initial configuration with the exactly same set-up,
you can get the same result
hi,it would be nice knowing the errors.
Francesco
2012/11/22, Steven Neumann :
> Dear Gmx Users,
>
> Is it possible to convert topology produced by Gmx and convert it ont
> the psf file? I used Justin script but when I load pdb and psf in VMD
> then there are some errors.
> Would you help?
>
> S
There was an error with index < 1 which this script assigned to bond
part. The script provided here:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/top2psf.pl
works much better.
Steven
On Thu, Nov 22, 2012 at 12:50 PM, francesco oteri
wrote:
> hi,it would be nice knowing th
Hi all,
I am planning to run a 100ns simulation by continuing a simulation in
increments of 1ns. After each round, analyses are performed and the
trajectory scrapped. One of the analysis I need to do is mean square
displacement; for this I need a continuous trajectory as provided by
trjconv -
Hi Pablo,
You can use trjcat to stitch the parts of your trajectory together.
A .cpt file contains information about the state, the positions and such.
It doesn't contain static information, like residue/atom names, which are
needed for a reference structure.
Cheers,
Tsjerk
On Thu, Nov 22, 201
yes,actually it works fine as long as you have one chain in you .top
file . if u have more subunits, u are supposed to merge the chains
using the appropriate value for -chainsep option in pdb2gmx
2012/11/22, Steven Neumann :
> There was an error with index < 1 which this script assigned to bond
>
Thanks for your reply, Tsjerk.
Indeed, trjcat is a good option. I could first run "trjconv -pbc nojump"
on a trajectory, then keep the last frame as a trr and stitch it with
the following trajectory; trjconv then takes the first frame as
reference for the nojump.
Regarding this, what would b
On 11/22/12 2:36 AM, rama david wrote:
Dear user ,
I simulate the two protein in random coil position, when they come close
they form antiparallel beta sheet structure.
I want to calculate the change in hydrophilic and hydrophobic surface
area over my simulation time.
For usig g_sas Shou
On 11/22/12 3:20 AM, junfang.zh...@csiro.au wrote:
Hi Justin
Thank you very much for your prompt reply!
I have used GROMACS96 force field to simulate pure coal density. It perfectly
matches the real coal density.
Now I want to apply this coal model to investigate gas adsorption in coal. Bu
On 11/22/12 5:44 AM, Kiwoong Kim wrote:
Hi,
It seems that the one directional diffusion constants can be obtained by
means of g_msd ...blabla...-type z.
However, my question is that I don't want to obtain the diffusion constants.
Actually, the MSD trajectory file for all 3 dimensional data c
Hi, all-
There are some issues with MTTK + constraints that are being worked
out for 4.6. The good thing is, I have developed some sensitive tests
of the correct volume distribution (see
http://arxiv.org/abs/1208.0910) and the errors in PR are very, very
small. I would recommend using md + PR for
Hi justin,
Thank you for reply.
As per your suggestion,
The whole protein should always be the group for the
surface calculation. Whatever subset of those atoms (i.e. residues of
interest) can be the output group.
So as per your suggestion I have to select the protein as my option
On 11/22/12 1:54 PM, rama david wrote:
Hi justin,
Thank you for reply.
As per your suggestion,
The whole protein should always be the group for the
surface calculation. Whatever subset of those atoms (i.e. residues of
interest) can be the output group.
So as per your suggesti
Hello,
This is a very nice and interesting work, Michael. Thank you for the efforts
you made in writing this paper. I hope you will publish it.
Best
Stephane
Hi, all-
There are some issues with MTTK + constraints that are being worked
out for 4.6.
Thank you justin
With best wishes and regards,
Rama David
On Fri, Nov 23, 2012 at 12:45 AM, Justin Lemkul wrote:
>
>
> On 11/22/12 1:54 PM, rama david wrote:
>
>> Hi justin,
>> Thank you for reply.
>> As per your suggestion,
>> The whole protein should always be the group fo
On 11/22/12 9:14 PM, Yun Shi wrote:
Hi everyone,
I thought this might have been discussed before, but a search did not
give me any information. So I was trying to convert a .txc trajectory
into separate PDB files. But when I issued the command with -seq, I
got:
---
It's in review with JCTC right now.
On Thu, Nov 22, 2012 at 2:19 PM, ABEL Stephane 175950
wrote:
> Hello,
>
> This is a very nice and interesting work, Michael. Thank you for the efforts
> you made in writing this paper. I hope you will publish it.
>
> Best
>
> Stephane
>
>
> ___
Dear all,
I'm trying to simulate a protein with artificial six histidine residues
added on the N-terminal. As all would know very well, it is common to have
His tag attached on protein for purification reasons, and is thought to
affect the protein's activity minimally. I'm suspecting that in my
I gratefully appreciate to your reply Justin.
You are right, it seems that g_msd provides the MSD.xvg file what I want
(in one direction).
I was confused before.
Thanks again.
2012/11/23 Justin Lemkul
>
>
> On 11/22/12 5:44 AM, Kiwoong Kim wrote:
>
>> Hi,
>>
>> It seems that the one directio
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