RE: AMBER: large changes in xyz coordinates

From: Sivakolundu, Sivashankar <>
Date: Mon, 18 Aug 2003 12:51:49 -0500

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 []
Sent: Saturday, August 16, 2003 11:07 PM
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 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:
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            |
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Aug 18 2003 - 19:53:00 PDT
Custom Search