Hi Guys,
I have a molecule with a nitrogen bonded to three carbons and one
proton. Can anyone tell me what parameters to use? I have looked
through the amber parameter file and can't find suitable parameters.
I'm not sure if it is probable, but if the N1 of cytidine were
protonated, it would be similar to my situation.
Many thanks,
Sam
On Sep 26, 2007, at 3:27 AM, [EMAIL PROTECTED] wrote:
Thanks for your help Alan, Yang, and Belquis!
Now I managed to get trajectory in which a droplet stays in the
middle of the simulation box while a surface moves below the
droplet. First I used trjconv to remove periodicity (-pbc nojump)
and then performed translational fit for the droplet (-fit
translational) and finally transferred all the translating surface
atoms back to the simulation box (-pbc -inbox).
However, there is still a problem with fitting procedure which is
performed in three dimension and hence the surface translates
upwards during the video. It should be quite easy to modify trjconv
so that the fitting is performed only for the xy coordinates (not
for the z coordinate perpendicular to the surface) but with my
programming skills I wasn't able to do that (actually I wasnt able
to find the correct lines). So I would like to know if someone has
made a such modification to trjconv (trjconv_d) or could help me to
do it?
Thanks,
Janne
Hello Janne,
this is what I usually do when my molecules cross the box or dance
all
around and it works for me:
I first do this with the "original" unmodified or fitted xtc or trr
file:
trjconv -f -o -pbc nojump
then i take the modified trr or xtc and do a fit:
trjconv -f -s -fit rot+trans
Belquis
Hello gmx-users!
I am trying to make a simulation video in which a water droplet is
rolling or sliding on a surface. Due to a periodic boundary
conditions
a droplet is not whole all the time but it disappears from the right
and appears from the left in cycles.
I think that I could create more visual video by removing the
lateral
motion of the center of mass of a droplet so that the droplet would
stay whole
in the middle of simulation window and the surface would translate
below the droplet. I am not exactly sure how realistic this kind of
video would be and would like to know if someone has better ideas?
If there are no better ideas I would need advices to be able to
create
a such trajectory or video. Right now I am struggling with trjconv
which might be suitable for this purpose. However, if I use the
droplet as a group for translational fit (-fit translation) I get
trajectory in which the whole system wanders strangly (laterally
(the
surface moves first to the left and then back to the right) and also
in perpendicular to the surface due to the lowering of the height of
the center of mass of the droplet during the simulation) and the
droplet wont stay whole in the middle of the box. Any ideas what I
am
doing wrong or how I would be able to get rid of even this lateral
wandering so that I could at least see how realistic this
procedure is?
Thanks for your time and help in advance,
Janne
------------------------------------------------------------------------------
Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101
Joensuu,
FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED]
------------------------------------------------------------------------------
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Samuel Coulbourn Flores, PhD
Altman Lab
Department of BioEngineering
Stanford University
[EMAIL PROTECTED]
650.644.8416
花山
科学者
生物工学部
スタンフォ一ド大学
スタンフォ一ド、カリフォルニア、米国
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