[gmx-users] the mdp file
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 5 06:08:21 CET 2008
Again, please keep all correspondence on the gmx-users list. If others have
better ideas than me, they will be able to weigh in :)
He, Yang wrote:
> Hi Justin,
>
> Actually, when I set the nsteps by 10, I found that disassociation about the two strands of DNA happened. Hence, in your views, what is the problem?
>
> However, when I set the nsteps by 100 or larger, it did not disassociate at all for the DNA,keeping original state. I just got confused about that.
>
All of this may be a result of statistical sampling or whatever conditions you
are imposing. If you are pulling the DNA apart or applying a high temperature,
then maybe this phenomenon can occur in a very short timeframe. Otherwise, I
simply find your whole situation strange, and without substantially more
information, it is hard for anyone to interpret your odd results.
Run several simulations of adequate length to see separation of your DNA
strands, under whatever conditions you deem appropriate. If you obtain a
reasonably consistent set of results, then you can be pretty confident about
what you are seeing. But just because one simulation doesn't necessarily
doesn't do the same thing as another does not necessarily indicate any
particular problem.
-Justin
> Yang
> ________________________________________
> From: Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Tuesday, November 04, 2008 7:06 PM
> To: He, Yang; Gromacs Users' List
> Subject: Re: [gmx-users] the mdp file
>
> 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 [jalemkul at vt.edu]
>> 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: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
>>> 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
>>>> _______________________________________________
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before posting!
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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 gmx-users at gromacs.org
>>> 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 gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>> --
>> ========================================
>>
>> 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
>
> ========================================
>
--
========================================
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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