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> On 9/12/2011 5:37 AM, Sławomir Stachura wrote:
>> Hi!
>> Thanks Mark for reply. When I calculated fractional diffusion constant from
>> mass weighted MSD of long simulation I get st
Hi!
Thanks Mark for reply. When I calculated fractional diffusion constant from
mass weighted MSD of long simulation I get sth about 0.05. But when I do the
same for centre of mass, considering that MSD is expressed in nm^2, the result
is 1.35. When I look into xvg file MSD of centre of mass is
ulation of different times. Is that
possible there is some bug in MSD? Because as for me it looks so
Hope to have someone join the discussion,
Slawomir
Wiadomość napisana przez Sławomir Stachura w dniu 2011-12-04, o godz. 22:38:
>
> Hi,
>
> I was just wondering how MSDs in Gro
Hi,
I was just wondering how MSDs in Gromacs are normalized. I am calculatiing MSDs
for my lipid system of different timesteps of simulation and I get much higher
results for centre of mass calculations in comparison to mass-weighted one.
And I thought about normalization issue, but I couldn'
Miło mi to słyszeć. W takim razie czekam na przesyłkę.
Pozdrawiam,
Sławomir Stachura
Wiadomość napisana przez gmx-users-requ...@gromacs.org w dniu 2011-11-25, o
godz. 12:00:
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Sławomir Stachura
Centre de Biophys
Hi GMX-Users,
I am analysing my POPC membrane simulation and I want to calculate average
fluctuation from mean postion of POPC lipids in perpendicular direction to
membrane surface (Z-direction) to grasp that kind of motion. I've searched
through mailing list and manual, but couldn't find any so
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No -it is not a typo - my cluster allows me to use higher amount of memory than
10%. Information I received from administrator of the cluster :
>> [root@isei ~]#top
>>
>> top - 13:52:23 up 30 days, 3:00, 76 users, load average: 5.85, 17.19,
>> 13.08
>> Tasks: 2825 total, 1 running, 2815 sleep
ran on?
>
> Cheers,
>
> Tsjerk
>
> 2011/6/27 Sławomir Stachura :
>> Hi GMX Users,
>> I am writting this email, beacause I think the g_msd program in Gromacs
>> 4.5.4 bears a problem. I was calculating the MSD od center of mass of POPC
>> in membrane (system
Hi GMX Users,
I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4
bears a problem. I was calculating the MSD od center of mass of POPC in
membrane (system contains 274 POPC lipid molecules in all-atom force field)
from 50 ns trajectory and it seems to consume great amou
Hi,
I have simulated fully hydrated POPC membrane for 50 ns and now I am analysing
if it's in equilibrated state. One of the needed by me parameters is fraction
of gauche dihedrals in acyl chains. I have tried g_angle, but it only shows
fraction of trans dihedrals. So is there possibility to c
Thank you very much for such quick reply. I misunderstood the meaning of
"iteration" . I've confused the iteration of LINCS algorithm with molecular
simulation step.
Best wishes,
Slawek
Wiadomość napisana przez Justin A. Lemkul w dniu 2011-05-18, o godz. 17:39:
&
Dear Users,
I am not sure if I understood properly how P-LINCS should parametrized for
simulation. In manual it's written that "one coordinate communication step is
required for the initial LINCS step and one for each iteration"; so as
coordinate communication is tightly binded to neighbor sea
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