AMBER Archive (2009)

Subject: Re: [AMBER] creating a restart file from md.out

From: oguz gurbulak (gurbulakoguz_at_gmail.com)
Date: Tue Feb 03 2009 - 07:22:45 CST

I created a ptraj input file as you said and run the script writing:
ptraj n-dodecane.prmtop < ptraj.in > n-dodecane.rest , but I couldn't get
the n-dodecane.rest file. Could you help me about it ?

Thanks in advance.

ptraj.in

trajin n-dodecane.equ.mdcrd 726000 726000
trajout n-dodecane.rest restart

2009/2/3 Carlos Simmerling <carlos.simmerling_at_gmail.com>

> the mdout file does not have coordinate information. that is in the mdcrd
> file.
> if you wrote to the mdcrd file at this step (if depends on your
> setting of ntwx), then
> you can use ptraj trajin/trajout to extract that frame to a restart file.
>
> let's say you want to extract frame 726 (your nstep is 726000 and
> perhaps you set ntwx to 1000)
> then you can do this inside a ptraj script
>
> trajin mdout 726000 726000
> trajout filename restart
>
> along with all of the other things needed for running ptraj, this is
> just part but I assume you've already learned ptraj)
>
>
>
> On Tue, Feb 3, 2009 at 5:44 AM, oguz gurbulak <gurbulakoguz_at_gmail.com>
> wrote:
> > Dear All,
> >
> > I want to extract the output informations for NSTEP = 726000 in target
> > Density =0.7636 , create a restart file for input and start a md from
> this
> > point with little time steps. Is
> > it possible to do this in Amber ? If so, what should I do to do this
> > operation ?
> >
> >
> >
> > NSTEP = 726000 TIME(PS) = 1452.000 TEMP(K) = 271.69 PRESS =
> > 350.4
> > Etot = 3756.1288 EKtot = 2374.7495 EPtot =
> > 1381.3794
> > BOND = 346.1359 ANGLE = 1656.2278 DIHED =
> > 677.9015
> > 1-4 NB = 456.8660 1-4 EEL = 384.6550 VDWAALS =
> > -1729.3428
> > EELEC = -411.0640 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 73.3705 VIRIAL = -206.8362 VOLUME =
> > 37038.6242
> > Density =
> > 0.7636
> > Ewald error estimate: 0.4255E-04
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> >
>
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