AMBER Archive (2003)

Subject: RE: AMBER: large changes in xyz coordinates

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Mon Aug 18 2003 - 13:26:27 CDT

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_at_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_at_scripps.edu]
>Sent: Saturday, August 16, 2003 11:07 PM
>To: amber_at_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_at_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_at_structbio.vanderbilt.edu

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