[gmx-users] trjcat -settime option

[m-hatake at jaist.ac.jp]

Thank you so much, Yang Ye.


Masa

From: Yang Ye <leafyoung81-group at yahoo.com>
Subject: Re: [gmx-users] trjcat -settime option
Date: Wed, 19 Apr 2006 21:00:59 +0800

> I missed this for last mail. The use of gmxcheck is to determine the 
> "welding" point. So trjconv -b {start_time} -e {end_time} could be 
> useful in cases like resuming from crash.
> 
> Yang Ye
> 
> $,3r}r}r}r}r}r}r}r}(B
> yes. you are right in both cases. BTW, I have one suggestion to you,
> "before trjcat", use gmxcheck to check the time in the trajectory.
> 
> Yang Ye
> 
> m-hatake at jaist.ac.jp wrote:
> > Thanks for quick reply, Yang Ye and David,
> >
> > But my way of asking seemed not good.
> >
> > I know what trjcat command is.
> > It is to concatinate two .trr files.
> > but when we use trjcat command with -settime option,
> > the command says as following,
> >
> >   
> >> c (continue) - The start time is taken from the end
> >> of the previous file. Use it when your continuation run
> >> restarts with t=0.
> >>
> >> l (last) - The time in this file will be changed the
> >> same amount as in the previous. Use it when the time in the
> >> new run continues from the end of the previous one,
> >> since this takes possible overlap into account.
> >>     
> >
> > I am confused which option I should use, either "c" or "l".
> >
> > We usually, I think, continue the simulation as
> > changing confout.gro to conf.gro, using grompp to make 
> > a new .tpr file, and mdrun.
> >
> > As a result, we have two .trr files.
> > In this case, when we concatinate two .trr files,
> > using trjcat command with -settime, we should select "c(continue)",
> > right?
> >
> > On the other hand,
> > Due to some computer failure, we usually use tpbconv command in order to
> > continue the simulation as Yang and David said.
> > In this case, after the simulation, when we concatinate two .trr files,
> > using trjcat command with -settime, should we select "l(last)"?
> >
> > Is this correct?
> >
> > Sorry for bothering you, but I appreciate you if you answer my question.
> >
> >
> > Best regards,
> > Masa
> > --
> > Masaomi Hatakeyama
> > Ph.D Candidate(Knowledge Science, JAIST)
> > m-hatake at jaist.ac.jp
> > http://www.jaist.ac.jp/~m-hatake
> >
> >
> >
> >
> > From: Yang Ye <leafyoung81-group at yahoo.com>
> > Subject: Re: [gmx-users] trjcat -settime option
> > Date: Wed, 19 Apr 2006 14:40:09 +0800
> >
> >   
> >> Hi,
> >>
> >> It seems that you got two questions:
> >> 1. concat several trajectory together, use trjcat.
> >> 2. use tpbconv.
> >>
> >> To use tpbconv, just use the last trajectory you have before the 
> >> computer failure. Also, to use tpbconv, you will need edr. I suggest you 
> >> to use gmxcheck to check both the trr and edr file to find their common 
> >> ending point.
> >>
> >> Yang Ye
> >>
> >> m-hatake at jaist.ac.jp wrote:
> >>     
> >>> Hello, again
> >>>
> >>> I'm sorry I had a mistake about my question.
> >>>
> >>>  When using tpbconv command to make a new topol.tpr and
> >>>  continue a simulation due to some computer problems(e.g. power failure),
> >>>  should I select _l_ option?
> >>>  
> >>>  When I change confout.gro into conf.gro and continue
> >>>  a simulation, should I select _c_ option?
> >>>
> >>> Best Regards,
> >>> Masa
> >>> --
> >>> Masaomi Hatakeyama
> >>> Ph.D Candidate(Knowledge Science, JAIST)
> >>> m-hatake at jaist.ac.jp
> >>>
> >>>
> >>> From: m-hatake at jaist.ac.jp
> >>> Subject: [gmx-users] trjcat -settime option
> >>> Date: Wed, 19 Apr 2006 12:57:28 +0900 (LDT)
> >>>
> >>>   
> >>>       
> >>>> Hi everyone,
> >>>>
> >>>> I'd like to ask a easy question today.
> >>>> (I didn't understand the command explanation 
> >>>>  because of my poor english skill)
> >>>>
> >>>> Please teach me the difference c(continue) and l(last)
> >>>> when using -settime option with trjcat command.
> >>>>
> >>>> I have several trajectory files and want to conbine them,
> >>>> but I have two types.
> >>>> one of them: changing confout.gro into conf.gro and continue the simulation.
> >>>> the other: using tpbconv command to make a new topol.tpr due to some 
> >>>> computer problems and continue the simulation.
> >>>>
> >>>> When using tpbconv command to make a new topol.tpr and
> >>>> continue a simulation due to some computer problems(e.g. power failure),
> >>>> should I use -l option?
> >>>>
> >>>> When I change confout.gro into conf.gro and continue
> >>>> a simulation, should I use -o option?
> >>>>
> >>>>
> >>>> If I don't use -settime option, what happen?
> >>>>
> >>>> Thanks in advance,
> >>>>
> >>>> Masa
> >>>> --
> >>>> Masaomi Hatakeyama
> >>>> Ph.D Candidate(Knowledge Science, JAIST)
> >>>> m-hatake at jaist.ac.jp
> >>>>
> >>>>
> >>>>
> >>>>
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