Hi Nadir,
First of all, nm / ps^2 for acceleration was not a choice, but a
consequence of other choices. Second, it's meaningless to pull this
out of context. There's no reason whatsoever not to have a huge
accelaration, if it is only for short times. It's the speed that
counts, not the accelerati
I've got a discrepancy calculating the diffusion coefficient via
Green-Kubo equation and via Einstein equation.
For methanol (200ps, dt=0.001):
frequency to write velocities = 5
frequency to write coordinates = 100
$ g_msd
2.3 (and it is true)
$ g_velacc -nonormalize -acflen 1001
$ g_analyze -f
On Sun, 15 Jun 2008 12:17:01 +0300
Vitaly Chaban <[EMAIL PROTECTED]> wrote:
I've got a discrepancy calculating the diffusion coefficient via
Green-Kubo equation and via Einstein equation.
For methanol (200ps, dt=0.001):
frequency to write velocities = 5
frequency to write coordinates = 100
Any
ANINDITA GAYEN wrote:
Please make more of an effort to follow conventions of written English -
like spelling, punctuation and capitalization. You're asking for free
help here, so you should make things easy for your reader. Following
conventions does that.
I want to simulate a peptide with
Thanks for Reply,
I am using 310k T for POPC Bilayer.I have found area per lipid 0.63nm^2/sec at
310k in gmx-archives. I have got the value 0.64522nm^2/sec and asked to
gmx-archvies people replied, that is reasonable value.
the reference value is right?
Thanks in advance
On Sat, 14 Jun 2008
Hi all,
I am having 7.25ns trajectory file , I am trying to pick up 6250ps
to 7250 ps trajectory file from whole trajectory by using trjconv,
Command line is
*trjconv -f 7.25ns.xtc -s pr.tpr -o 6.25_7.25_out.trr -b 6250
-e 7250
selected " system " for getting output
it s
sudheer babu wrote:
Hi all,
I am having 7.25ns trajectory file , I am trying to pick up
6250ps to 7250 ps trajectory file from whole trajectory by using trjconv,
Command line is
*trjconv -f 7.25ns.xtc -s pr.tpr -o 6.25_7.25_out.trr -b
6250 -e 7250
selected " system
I am having the evidence that I have drawn RMSD plot for 7.25ns
simulation, in rmsd.xvg file showed the values of the time(ps),
mentioned in *trjconv command
Im pasting my .mdp file
title = dpt_prod
constraints = hbonds
integrator = md
dt = 0.00
>>For methanol (200ps, dt=0.001):
>> frequency to write velocities = 5
>> frequency to write coordinates = 100
XP> Any rationale behind this difference? That might well result in differences
XP> of C(t) at short times.
Yes, the difference is dictated by the pure logic.
>> $ g_msd
>> 2.3 (and it i
On Sun, 15 Jun 2008 19:07:48 +0300
Vitaly Chaban <[EMAIL PROTECTED]> wrote:
For methanol (200ps, dt=0.001):
frequency to write velocities = 5
frequency to write coordinates = 100
XP> Any rationale behind this difference? That might well result in
differences of C(t) at short times.
Yes, the d
Hi,
On Sunday, 15. June 2008 18:12, sudheer babu wrote:
> I am having the evidence that I have drawn RMSD plot for 7.25ns
> simulation, in rmsd.xvg file showed the values of the time(ps),
> mentioned in *trjconv command
>
> Im pasting my .mdp file
>
> title = dpt_prod
> constraints
sudheer babu wrote:
I am having the evidence that I have drawn RMSD plot for 7.25ns simulation, in rmsd.xvg file showed the values of the time(ps), mentioned in *trjconv command
That's evidence if you used the .xtc file for producing that RMSD plot
and the full system was used for the RMSD
Xavier,
Ones more. The length of the trajectory is 200ps (200 000 time steps).
Certainly, both for
velocities and displacements. I can ensure this is enough to obtain
correct values, no matter Einstein or Green-Kubo formula one uses.
Moreover, if you carry out a simulation for 1000ps, nothing wil
dear users
I have encouneterd a problem with mpirun I have 2 pc (every pc has 1 intel
quad core cpu) ,when I run mdrun on 1 machine with "-np 4 " option the
calculation
run on 4 cores and goes faster ,system monitor show all 4 cores of this
cpu are working
every core has 90%
On 15.06.2008, at 20:19, ha salem wrote:
dear users
I have encouneterd a problem with mpirun I have 2 pc (every pc
has 1 intel
quad core cpu) ,when I run mdrun on 1 machine with "-np 4 "
option the calculation
run on 4 cores and goes faster ,system monitor show all 4 cores
Let me summarize the conflict in this example:
The acceleration to be applied corresponds to 2x10^12 meter/(second squared)
(in words: two times ten to twelve) which means in vacuum that water molecule
may gain two times ten to twelve meter/second velocity at every second (e.g.
for dilute cas
Hi All,
I have MD simulation which crashed and I combine the frames with trjconv. Now
the problem is that when I do analysis like that of Solvent accessible surface
area, it showed that the incomplete frame . I use the gmxcheck with the
following result
d 1: 'Protein'
1695 out of 2854 atoms were
Dear gmx-users,
I have installed the gromacs 3.3.3 on a dual core HP workstation with
Ubuntu platform. All the programs are properly installed and working
except ngmx and dssp. However there is a difference, ngmx is not
installed as I donot see the link in /usr/local/bin along with the
oth
s lal badshah wrote:
Hi All,
I have MD simulation which crashed and I combine the frames with
trjconv. Now the problem is that when I do analysis like that of Solvent
accessible surface area, it showed that the incomplete frame . I use the
gmxcheck with the following result
d 1: 'Protein'
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