Please remember to keep all correspondence on the list.
He, Yang wrote:
Hi Justin,
I just use the command ngmx to show the figure and hope to get the animation
about the two strands' disassociation of DNA model. But I found it just work
when I set the value of nsteps by 10 and for other larger value, no animation
exists, just a static figure. Also, I have tried to reduce the value of time
step and the situation is the same.
Like I said before, 10 steps is too short of a simulation time to see any major
changes in your system. If you've got a dt = 0.002 ps, then you've only
simulated for 0.02 ps! No major conformation changes are likely to happen in
that amount of time. If you're seeing something after 10 steps, it may be an
anomaly. Other than that, I have no idea what's going on.
-Justin
How I can solve this problem and get the correct animation ? Thank you .
Yang
________________________________________
From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Tuesday, November 04, 2008 6:54 PM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] the mdp file
He, Yang wrote:
Hi Justin,
I have changed the value of nsteps(>100) and the nstout(=1), but I found that
there is just the static figure and no animation .
What are you using for visualization?
it always shows that :Last frame 0 time 0.000
What tool are you using that is showing this?
-Justin
What is the problem?
Thank you for your reply.
Yang
________________________________________
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL
PROTECTED]
Sent: Monday, November 03, 2008 4:22 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the mdp file
He, Yang wrote:
Hi all users,
When I change the value of nsteps in my mdp file to run the gromacs and show
the trajectory in the gromcas, I found that only the value of nsteps is set by
10, is there just the animation of the molecule's movement . I have tried many
time and set the other values of nsteps, there isn't any movement about the
molecule at all.
I'm not quite clear on what the problem is. But you should be aware that 10
steps (0.02 ps in your case!) is an exceedingly short timeframe under any
circumstances.
If what you've shown is your full .mdp file, then the other values will be taken
as default. For output (nstxout) this value is 100. So you will likely only
see the starting and ending coordinates of your 10-step simulation.
Try a longer simulation (>100 steps) or specify nstxout = 1 and see if you
generate 10 frames.
-Justin
I am strange about that and this is my part of mdp file:
;VARIOUS PREPROCESSING OPTIONS
title = atom
; Preprocessor - specify a full path if necessary.
cpp = cpp
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 10
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 1
; ns algorithm (simple or grid)c 4
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 0.686
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = User
rcoulomb-switch = 0
rcoulomb = 0.9
; Relative dielectric constant for the Cut-off or DC of the reaction field
epsilon-r = 78
; Method for doing Van der Waals
vdw-type = User
; cut-off lengths
rvdw-switch = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
Can anyone of you tell me what is the problem?
Thank you very much.
Yang
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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