I've just been doing that, but as you say, ptraj gets rid of the
velocities so you have to cut and paste them back in!
James.
On Mon, 18 Aug 2003, Kristina Furse wrote:
> Date: Mon, 18 Aug 2003 13:26:27 -0500
> From: Kristina Furse <kristina.e.furse.vanderbilt.edu>
> Reply-To: amber.scripps.edu
> To: "Sivakolundu, Sivashankar" <Sivashankar.Sivakolundu.stjude.org>,
> amber.scripps.edu
> Subject: RE: AMBER: large changes in xyz coordinates
>
> You could use ptraj to image a frame from before the crash and generate a new
> restart file, but whenever I've done this I've lost the velocities. Maybe
> someone knows how to avoid this?
>
> Kristina
>
>
> >===== Original Message From "Sivakolundu, Sivashankar"
> <Sivashankar.Sivakolundu.stjude.org> =====
> >Dear Dr. Case,
> >Thank you for the reply. I think it was due to non-removal of translational
> motion (by setting nscm=0), since a test simulation I did with default nscm
> doesn't change coordinates much.
> >Now that the damage is done to my long simulation, is it possible to restart
> the calculation using coordinates from the trajectory file just before the
> crash? I tried to just put together a new restart file from the coordinates
> and velocities of
> >the system ~1 ns before the crash (from the trajectory file) but neither
> sander nor carnal could read in the coordinates. I think this is mainly b'cos
> of the large values for xyz coordinates, since a similar restart file created
> using the
> >coordinates and velocities at very early stage of simulation was read fine by
> sander and carnal.
> >Is there any way I can restart the simulation using the
> coordinates/velocities obtained from trajectory file?
> >
> >Thank you very much
> >Siva Sivakolundu
> >
> >-----Original Message-----
> >From: David A. Case [mailto:case.scripps.edu]
> >Sent: Saturday, August 16, 2003 11:07 PM
> >To: amber.scripps.edu
> >Subject: Re: AMBER: large changes in xyz coordinates
> >
> >On Sat, Aug 16, 2003, Sivakolundu, Sivashankar wrote:
> >
> >> I'm trying to do an constant pressure md simulation of a protein solvated
> in
> >> a water box using Amber 7 for several nanoseconds. The simulation went fine
> >> until it was around 8 ns and then it crashed without any error message. I
> >> couldn't restart the simulation since the restart file didnt seem to have
> >> any coordinates (see below), though the values for velocities looked fine.
> >
> >You should certainly visualize your trajectory to see what is going on...
> >my guess is that some problem will be obvious, if all of the coordinates
> >are getting extremely large.
> >
> >You set nscm to 0, which disables removal of center-of-mass translational
> >motion...it is probably better to leave this at its default value.
> >
> >If the program crashed in the middle of a run (you don't say) I don't know
> >why that would happen. But it looks like somehow you generated some
> >translational motion in the system during equilibration, and never removed
> >any of it.
> >
> >.hope this helps...dac
> >
> >--
> >
> >==================================================================
> >David A. Case | e-mail: case.scripps.edu
> >Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> >The Scripps Research Institute | phone: +1-858-784-9768
> >10550 N. Torrey Pines Rd. | home page:
> >La Jolla CA 92037 USA | http://www.scripps.edu/case
> >==================================================================
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> ****************************************************
> Kristina E. Furse
> Department of Chemistry
> Center for Structural Biology
> Vanderbilt University
> email: kfurse.structbio.vanderbilt.edu
>
>
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Received on Mon Aug 18 2003 - 19:53:00 PDT
