AMBER Archive (2009)

Subject: Re: [AMBER] is rst file the last structure?

From: Jason Swails (jason.swails_at_gmail.com)
Date: Sat Nov 14 2009 - 11:18:22 CST

The problem is that you are not getting the last structure from your trajin
statement.

trajin 1 1000 1000 will pull snapshots 1 through 1000 in increments of
1000. Thus, it will give you restart files corresponding to snapshot 1,
1001, 2001, 3001, etc. However, there is no 1001, so it stops with 1.
Thus, the snapshot you're getting is the very first one.

To do what you say you're trying to do, modify your trajin statement as
follows:

trajin 1000 1000 1

Which will pull snapshots 1000 to 1000 by increments of 1 (or just snapshot
1000). One warning, though, is that I think mdcrd files and restart files
are saved with different levels of precision in the x,y,z coordinates of
each atom, so the files may appear to be different, but visualizing both
should show you that they are essentially identical.

Hope this helps.

All the best,
Jason

On Fri, Nov 13, 2009 at 11:52 PM, qiaoyan <qiaoyan_at_dicp.ac.cn> wrote:

> dear all:
> the script I used in npt simulation is as follows:
>
> &cntrl
> imin=0,
> ntx=5, irest=1,
> ntpr=100, ntwx=1000,ntwr=5000,
> dt=0.002,nstlim=1000000, nscm=1000,
> cut=9.,dielc=1.0,
> ntc=2, ntf=2,
> ntb=2, iwrap=1.0,
> ntp=1,pres0=1.0,taup=3.0,
> ntt=1, tautp=3.0,temp0=300.0,
> ioutfm=1
> /
> I use the rst file to generate the pdb file a, I think a is the structure
> of 2ns(the 1000th strcture), then I use ptraj to generate the 1000th
> structure (trajin nptm501.dcd 1 1000 1000,trajout b.pdb pdb), but when I
> compare the two structures a and b, they differ significantly. what is wrong
> with the problem?
>
> 2009-11-14
>
>
>
> qiaoyan
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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