Re: [AMBER] Serious problem at specific time point

From: Hoshin Kim <>
Date: Thu, 11 Nov 2010 16:31:01 +0900

Dear AMBER specialists,

Thank you all.
I updated AMBER 11 with the latest bug-fixed version. Now I'm trying to
restart my simulation from the timestep which shows wrong results.
But I don't know how to extract restrt file well.
When I ran PTRAJ like as below to make restrt file, it lost their velocity
Trajin md.x 8200 8200 1
Trajout md_new.restrt restart

So, I changed some parameters in production MD protocol to get correct
NTX = 5 -> 1
Tempi = 300 -> 0
Irest =1 -> 0

After short time simulation using changed restart file and protocol, I
merged two trajectories (original 8.2ns + new 20ps ), then analyzed RMSd
plot. But slope was dropped down suddenly at merged point. ( I attached a
plotting data)

How can I get correct velocity, or
Could anyone tell me how can I restart simulation at middle of point with no
Thanks in advance,

Hoshin Kim,

                   Hoshin Kim
Visiting Scholar
Department of Chemical and Biomolecular Engineering
North Carolina State University
Raleigh, NC 27695
Phone: 919-986-9258
Graduate student (M.D. candidate)
Ionic Liquids Team(ILs) in Bio Nano Process Lab
Department of Biological Engineering,
2S 113, Engineering building Inha University,
253 Yonghyeon Dong, Nam Ku
Incheon, KOREA
TEL) +82-32-860-8655

-----Original Message-----
From: Jason Swails []
Sent: Thursday, November 11, 2010 10:47 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Serious problem at specific time point

Ah, forgot about this.

The bugfix is already posted:



On Wed, Nov 10, 2010 at 6:09 PM, Thomas Cheatham III <> wrote:

> > When I calculated RMSd of catalytic domain of enzyme, slope was
> > suddenly soared at 4.8ns (I attached a plotting data). So I ran the
> > VMD to
> visualize
> > what happened at this point, as I attached, protein structure was
> suddenly
> > collapsed at that point !
> ...
> > This is my second try. This problem was occurred at almost same
> > point
> when I
> Let me guess: ascii trajectory, > 2 GB, trajectory was imaged/rms fit
> with ptraj from AmberTools prior to viewing it? This is a bug that
> plagued me until yesterday; fixed by Dan Roe and it is working it's
> way through the bugzilla chain and hopefully soon to the bugfix page...
> To get around this for now, use an earlier version of ptraj (amber10)
> or get the older standalone version from:
> --tec3
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
AMBER mailing list
Received on Thu Nov 11 2010 - 14:00:03 PST
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