[gmx-users] trjcat -settime option

[m-hatake at jaist.ac.jp]

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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