Dear users,
I am comparing different schemes for computing the self-diffusion of a
system. One of the approches
I am considering is using block averages.
I have a 50 ns long trajectory and I want to compute the
block-averaged diffusion constant as follows:
(1) Divide the trajectory into blocks o
- Original Message -
From: ms
Date: Monday, August 30, 2010 10:15
Subject: Re: [gmx-users] Re: NPT simulation
To: jalem...@vt.edu, Discussion list for GROMACS users
> On 29/08/10 19:39, Justin A. Lemkul wrote:
>
> >When dividing the energy of a system by the number of molecules
> (in
ms wrote:
On 29/08/10 19:39, Justin A. Lemkul wrote:
When dividing the energy of a system by the number of molecules (in a
homogeneous system), you are extracting what I believe is commonly
referred to as "configurational energy" which, for relatively simple
systems, should converge fairly qu
- Original Message -
From: pawan raghav
Date: Friday, August 27, 2010 17:22
Subject: [gmx-users] contact residues
To: gmx-users@gromacs.org
> I have used g_mdmat
g_mdmat -f traj.xtc -s md.tpr -mean dm.xpm -frames dmf.xpm -no num.xvg >
> I got dm.xpm graph which shows mean of whole si
On 29/08/10 19:39, Justin A. Lemkul wrote:
When dividing the energy of a system by the number of molecules (in a
homogeneous system), you are extracting what I believe is commonly
referred to as "configurational energy" which, for relatively simple
systems, should converge fairly quickly. The re
- Original Message -
From: abdullah ahmed
Date: Friday, August 27, 2010 20:28
Subject: [gmx-users] Internal Density
To: gmx
---
|
> Dear all,
>
> I have 2 structures similar to a Beta-turn where the inside is hydrophobic
- Original Message -
From: Sai Pooja
Date: Monday, August 30, 2010 3:33
Subject: Re: [gmx-users] LJ potential
To: Discussion list for GROMACS users
> Hi, >
> I am simulating a system of a protein in water. I am trying to run the
> simulation with a modified protein-water LJ and
- Original Message -
From: Moeed
Date: Monday, August 30, 2010 9:09
Subject: [gmx-users] energy unit
To: gmx-users@gromacs.org
> Dear Justin,
>
> Thanks for your explanation. I am sorry to bother you again. Like you said:
> "a mole of a given species in the given configuration would h
alexander yakovenko wrote:
Hi Justin!
Thank you for replay. My histogram (can send if required) consists of 13
windows (0.1 and 0.2nm sampling) and look like two peaks (with
amplitudes 3-4e+2) separated with a valley of 1.2-1.5e+2 (my protein has
two sub-domains so should be OK) and smalle
Moeed wrote:
Dear Justin,
Thanks for your explanation. I am sorry to bother you again. Like you
said: "a mole of a given species in the given configuration would have
this energy in kJ". This is absolutely clear but actually I think
increasing the total energy with system size contradict th
Dear Justin,
Thanks for your explanation. I am sorry to bother you again. Like you said:
"a mole of a given species in the given configuration would have this energy
in kJ". This is absolutely clear but actually I think increasing the total
energy with system size contradict this statement unless
Hi Justin! Thank you for replay. My histogram (can send if required) consists
of 13 windows (0.1 and 0.2nm sampling) and look like two peaks (with amplitudes
3-4e+2) separated with a valley of 1.2-1.5e+2 (my protein has two sub-domains
so should be OK) and smallest overlap between windows is 1e
Moeed wrote:
Hello Dr. Chaban,
System size is 5 *5*3 nm when density reaches around 600 SI. Can you
please explain what do you mean by "What about dependence heat of
evaporation vs system size ?". I dont know how to compute vap. heat in
gromacs!
Unfortunately, I am still unclear about ene
Hello Dr. Chaban,
System size is 5 *5*3 nm when density reaches around 600 SI. Can you please
explain what do you mean by "What about dependence heat of evaporation vs
system size ?". I dont know how to compute vap. heat in gromacs!
Unfortunately, I am still unclear about energy units. :(
Yes, on
Hi,
I am simulating a system of a protein in water. I am trying to run the
simulation with a modified protein-water LJ and coulomb interaction. Since
LJ and coulomb interaction parameters are defined at the atomic level in
the forcefield files, I cannot figure out a good way to modify them for
pr
- Original Message -
From: nur avneet
Date: Friday, August 27, 2010 14:40
Subject: [gmx-users] using gromacs for peptpoids
To: gmx-users@gromacs.org
---
| > hello all > > can we use gromacs G43A1 or ggmx ff for simulations of
pe
- Original Message -
From: NG HUI WEN
Date: Friday, August 27, 2010 15:55
Subject: [gmx-users] Attempting to scale gromacs mdrun_mpi
To: gmx-users@gromacs.org
---
|
> Thanks a lot Roland! > > I'm using Beowulf clus
- Original Message -
From: poj...@icp.uni-stuttgart.de
Date: Saturday, August 28, 2010 2:11
Subject: [gmx-users] Saving velocities
To: gmx-users@gromacs.org
> Hi,
>
> Does anybody knows how to save the velocities of a group of particles
> every N time steps without having to write the .
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