AMBER Archive (2003)

Subject: AMBER: Restarting MD amber7

From: raist_at_mmb.pcb.ub.es
Date: Mon Nov 17 2003 - 12:54:32 CST

Hi all,
the other day I posted a mail regarding problems restarting MD with
amber7. I was running TGMD on a DNA+ions+water and after 8ns sander
complained with the usual SHAKE problem (when visualizing the structure it
was fine but the 2 strands were not imaged together). I checked the
energies to see there were no flying ice cube or other artifacts during
the simulation.

 When I image the last step of the previous run and start the simulation
from there (with the corresponding velocities) sander does not complain.
It does not complain either when I use the non-imaged restart file turning
off TGMD and using amber 7 and amber 6. So I guess the problem comes from
TGMD when you implement the restrains to target atoms and it needs to
compare to the reference structure. Has anyone had similar problems??? Do
you think this is really the problem??

Thanks in advance.

----------------------------------------------------------------
Alberto Perez
Molecular Modeling & Bioinformatics group

IRBB Parc Cientific de Barcelona | e-mail:raist_at_mmb.pcb.ub.es
Universitat de Barcelona | phone: + 34 93 403 71 55
Josep Samitier,1-5 | FAX: + 34 93 403 71 57
08028 Barcelona (Spain) |

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