AMBER Archive (2006)

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

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sun Nov 05 2006 - 00:31:25 CST

After "rms first out t1eq.rms :1-388_at_CA,C,N", please
add the time interval that the computer store the crd
file.

Best regards.

Fenghui Fan

--- Adrian Roitberg <roitberg_at_qtp.ufl.edu> wrote:

> Have you checked the file t1eq.rms to see what is in
> there ? That is
> where you asked ptraj to dump the rms data vs time.
>
>
>
> r. a. wrote:
> > Dear Amber Users
> >
> > 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
> > my ptraj file is:
> >
> > trajin heat4.crd
> > trajin eq4.crd
> > trajin md4.crd
> > rms first out t1eq.rms :1-388_at_CA,C,N
> > strip :WAT
> > go
> >
> > It would be grateful if anyone provide me with
> some more information about this problem. I checked
> the amber archive & tried to use that but it wasnt
> successful.
> >
> > Regards
> >
> >
> >
>
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project and Department
> of Chemistry
>
> University of Florida PHONE
> 352 392-6972
> P.O. Box 118435 FAX
> 352 392-8722
> Gainesville, FL 32611-8435 Email
> adrian_at_qtp.ufl.edu
>
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>
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> or that we are to stand by the president right or
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> to the American public."
> -- Theodore Roosevelt
>
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