Dear all,
I am simulating a binary system of two non mixing components (5CB and water
using version 4-0-3; the whole equilibrated trajectory is about 300ns).
I want to calculate the rdf of the centers of mass of 5CB using the command
g_rdf -f traj300.xtc -rdf mol_com -o rdf_com_300.xvg -no
> Date: Tue, 9 Mar 2010 10:39:01 +0100
> From: er...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] rdf problem
>
> Antonia V. skrev:
> > Dear all,
> >
> > I am simulating a binary system of two non mixing components (5CB and
>
Dear all,
I am simulating a binary system of two non mixing components (5CB and water
using version 4-0-3; the whole equilibrated trajectory is about 300ns).
I want to calculate the rdf of the centers of mass of 5CB using the command
g_rdf -f traj300.xtc -rdf mol_com -o rdf_com_300.xvg -noxvg
Dear all,
I am simulating a two component system (which form two completely separated
phases) and I want to calculate the g(r) of the centers of mass of the one
component.
Using the command,
g_rdf -f traj.xtc -rdf mol_com
I get an rdf which doesn't obtain the value one at long distances.
Dear all,
I am simulating a two component system and I want to calculate the g(r) of the
centers of mass of the one component.
Using the command,
g_rdf -f traj.xtc -rdf mol_com
I get an rdf which doesn't obtain the value one at long distances. How can I
change that?
thank you for your help,
> > I am trying to simulate a two component system, and I would like to ask
> > you the two following questions:
> >
> > 1) Is it possible to use a different scaling factor (for the LJ and the
> > electrostatics) for each component?
>
> Not natively. How would you like to treat non-bonded int
Dear all,
I am trying to simulate a two component system, and I would like to ask you the
two following questions:
1) Is it possible to use a different scaling factor (for the LJ and the
electrostatics) for each component?
2) Is it possible to use energy and pressure correction only for th
Dear all,
I am trying to simulate a two component system, and I would like to ask you the
two following questions:
1) Is it possible to use a different scaling factor (for the LJ and the
electrostatics) for each component?
2) Is it possible to use energy and pressure correction only for the o
Unfortunately, it' s the only way I can do it, since I want two completely
separated phases.
With the tools provided by GROMACS I get a mixture, is there a way to get a box
with two separated phases?
Antonia
_
Show them the way!
> Date: Fri, 8 May 2009 19:38:41 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] (no subject)
>
> Antonia V. wrote:
> > Dear all,
> >
> > I am trying to simulate a water-liquid crystal system. My initial is box
Hi,
I just put one box on top of the other in order to make my new system.
I use no constraints for the system, and I can't figure out the problem. It
seems that the water molecules of the new system are getting crazy...
Antonia
_
Dear all,
I am trying to simulate a water-liquid crystal system. My initial is box is
creating by merging two well equilibrated boxes of water and LC. After a steep
simulation of about 1,000,000 steps I try to do an md simulation but I get the
error
"Water molecule starting at atom 9103 can no
Dear all,
I am trying to do an md simulation of a system consiting of water and liquid
crystalline molecules, starting from a random initial configuration.
After some energy minimization if I try to do an NVT simulation (I use the
VERSION 4.0.3) I get the error
t = 0.000 ps: Water molecule st
At the beginning of your md.mdp file you will see the following:
; RUN CONTROL PARAMETERS
integrator = steep
With this command you ask GROMACS to energy minimize your system by steepest
descent.
If you want to run a md simulation you will have to change the intergrator to
md.
Yo
I switched to v-rescale for the thermostat and things look normal!
Thanks for the help
Antonia
> Date: Wed, 1 Apr 2009 12:11:47 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] (no subject)
>
>
>
> Antonia V. wrote:
> > >
hoover thermostat (340K)
> 5. Which Gromacs version you are using
I use GROMACS 4.0.3
Thank you
Antonia
> Date: Wed, 1 Apr 2009 06:39:17 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] (no subject)
>
>
>
> Antonia V. wrote:
&g
Hello,
I am trying to simulate a system at the NVT ensemble, but after a few steps I
get the error
[compute-0-4:01361] *** Process received signal ***
[compute-0-4:01361] Signal: Segmentation fault (11)
[compute-0-4:01361] Signal code: Address not mapped (1)
[compute-0-4:01361] Failing at addre
Did you try g_angle??
Antonia
Date: Wed, 1 Apr 2009 11:35:29 +0530
From: venkat...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] How to calculate the dihedral angle variations ???
Hi Everyone !
How can i see the variations in the "Cβ-S-S-Cβ"
(Disulfide bridge) dihedral angle during
artificially small???
I think I will have to read some things about Berendsen and PR.
Thanks
Antonia
> Date: Tue, 24 Mar 2009 11:09:07 +0100
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] (no subject) - fluctuations
>
> Antonia V
24 Mar 2009 09:49:45 +0100
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] (no subject) - fluctuations
>
> Antonia V. wrote:
> > Hello,
> >
> > So a I can either increase my system size or do some post
> > precessing-s
Hello,
So a I can either increase my system size or do some post
precessing-smoothing...
Thanks for the ideas
Antonia
> Date: Tue, 24 Mar 2009 11:39:19 +1100
> From: dallas.war...@pharm.monash.edu.au
> Subject: RE: [gmx-users] (no subject) - fluctuations
> To: gmx-users@gromacs.org
>
> > > Is
Hello,
Is there a way to reduce the fluctuations of the properties calculated with
g_energy?
Thanks
Antonia
_
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Hello,
sorry to ask again, but I wander if the output files (axis1.dat,axis2.dat and
axis3.dat) of the g_principal program refer to Ixx, Ixy, Ixz, Iyx, Iyy, Iyz,
Izx, Izy, Izz components respectively.
Thank you
Antonia
_
Inv
> Date: Thu, 19 Mar 2009 11:51:51 +0800
> From: xouy...@uvm.edu
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Questions About Gromacs
>
> Hi, there are 3 questions I want to ask.
>
> 1. I run the md from the pdb file successfully and get a .trr trajectory
> file. But when I load the .trr
Hello,
I want to calculate the moments of inertia of a system of liquid crystals.
Using the tool g_gyrate I get 5 values. The three last values are called I1, I2
and I3. I suppose that they are Ixx, Iyy and Izz respectively. Is that correct?
What about the second column which is called Itot. Wh
Thank you
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] center of mass
Date: Mon, 16 Mar 2009 17:56:16 +0100
On Mar 16, 2009, at 5:51 PM, Antonia V. wrote:Hello,
I am wondering if there is a tool implemented in GROMACS that computes the
coordinates of the center
Hello,
I am wondering if there is a tool implemented in GROMACS that computes the
coordinates of the center of mass of each molecule of a simulation box.
Thank you
Antonia
_
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