AMBER Archive (2006)

Subject: Re: AMBER: PTRAJ RMS: dumping RMSd vs time data

From: Thomas Cheatham (
Date: Mon Nov 06 2006 - 22:18:20 CST

> I heated up my system slowly from 0-375K, when I checked density,
> pressure,temperature, kinetic & potential , & total energy, it seemed
> everything is fine with the system during the simulation but when I m
> sending the trajectory files to ptraj I always have this error: PTRAJ
> RMS: dumping RMSd vs time data

I am a little confused here; what is the problem? The above is just
stating that, as per the command,

> rms first out t1eq.rms :1-388_at_CA,C,N

The RMSd vs. time is being dumped (printed) out to the file t1eq.rms.

Does the program hang at this point (suggesting the "go" wasn't
recognized or no EOT (^D) was detected)?

Is the file not produced or is the data "funny"?

I think things are OK...

> Set 1950 .................................................
> Set 2000
> PTRAJ: Successfully read in 2080 sets and processed 2080 sets.
> Dumping accumulated results (if any)
> PTRAJ RMS: dumping RMSd vs time data

(everything looks OK)

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