[gmx-users] time step in gromacs 3.3

[David]

On Mon, 2005-11-07 at 12:24 -0600, Qing Zhu wrote:
> Yang Ye wrote:
> 
> > Qing Zhu wrote:
> >
> >> Hi David
> >>
> >> I tried to run 3.2.1 tpr with 3.3 using 3 fs as the time step, but 
> >> the simulation still crashed after several thousand steps. I have no 
> >> idea why there is huge differece between 3.2.1 tpr and 3.3 tpr, 
> >> because all the initial conditions are the same except the gromacs 
> >> version. Any suggestion?
> >
> > decrease the time step?
> 
> That's the thing I am curious about. With 3.2.1 I can even use 4 fs as 
> the time step, but with 3.3  3 fs would make the simulation crash.
If the same tpr from 3.2.1 works with 3.2.1 and crashes really fast with
3.3 then please open a bugzilla and upload the tpr file.


> 
> >>
> >> Thanks
> >> Qing Zhu
> >>
> >> David wrote:
> >>
> >>> On Fri, 2005-11-04 at 16:01 -0600, Qing Zhu wrote:
> >>>  
> >>>
> >>>> Hi David,
> >>>>
> >>>> What I did is to run 3.2.1 tpr files with 3.2.1, and run 3.3 tpr 
> >>>> files with 3.3.
> >>>>   
> >>>
> >>> Try 3.2.1 tpr with 3.3
> >>>
> >>>  
> >>>
> >>>> The results of gmxcheck have hundreds of pages, and I don't know 
> >>>> what could I get from gmxcheck.
> >>>>   
> >>>
> >>> See whether the difference is in the tpr or in mdrun.
> >>> If you have hundreds of page (pipe it through more) it may mean that 
> >>> you
> >>> are using a different force field, different coordinate/velocities 
> >>> which
> >>> means you can  not compare the simulations.
> >>>
> >>>
> >>>  
> >>>
> >>>> Thanks
> >>>> Qing Zhu
> >>>>
> >>>>
> >>>> David wrote:
> >>>>
> >>>>   
> >>>>
> >>>>> On Fri, 2005-11-04 at 15:25 -0600, Qing Zhu wrote:
> >>>>>
> >>>>>
> >>>>>     
> >>>>>
> >>>>>> Hi, everyone
> >>>>>>
> >>>>>> I tried to run lipid membrane simulations by setting the time 
> >>>>>> step to be 3 fs using gromacs-3.3,  and my simulations always 
> >>>>>> crashed after a short time unless I changed the time step back to 
> >>>>>> 2 fs. But if I run the same lipid membrane simulations using 
> >>>>>> gromacs-3.2.1, I can even use 4 fs as time step and the 
> >>>>>> simulations runs fine. It is not a big problem for me, but I am 
> >>>>>> just curious that why gromacs-3.3 is so critical about the time 
> >>>>>> step. Any one has an idea?
> >>>>>>  
> >>>>>>       
> >>>>>
> >>>>> Did you try running your 3.2.1 tpr file with 3.3 ? Did you compare 
> >>>>> 3.2.1 and 3.3 tpr files (using gmxcheck)?
> >>>>>
> >>>>>
> >>>>>     
> >>>>>
> >>>>>> Thanks
> >>>>>> Qing Zhu
> >>>>>> _______________________________________________
> >>>>>> gmx-users mailing list
> >>>>>> gmx-users at gromacs.org
> >>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>>>>> Please don't post (un)subscribe requests to the list. Use the www 
> >>>>>> interface or send it to gmx-users-request at gromacs.org.
> >>>>>>  
> >>>>>>       
> >>>>>
> >>>> _______________________________________________
> >>>> gmx-users mailing list
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> >>>>   
> >>>
> >>
> >> _______________________________________________
> >> gmx-users mailing list
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> >>
> >
> > -- 
> > /Regards,/
> > Yang Ye
> > /Computational Biology Lab
> > School of Biological Sciences
> > Nanyang Technological University
> > Singapore
> > Tel: 6316-2884
> > /
> >
> >------------------------------------------------------------------------
> >
> >_______________________________________________
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> >
> 
> Thanks
> Qing Zhu
> _______________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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