AMBER Archive (2003)

Subject: AMBER: Problems restarting with sander

From: raist_at_mmb.pcb.ub.es
Date: Fri Nov 14 2003 - 15:26:07 CST

HI everybody,
I'm running a MD on a 8-MER DNA using amber7. I restart the simulation
with coordinates and velocities from the previous run every 200ps. On one
of this restartings the MD died because of a large deviation between two
atoms(common SHAKE error)

When I looked at the restart file the two DNA strands, they are not imaged
together so what I did was to run ptraj with this:

trajin coord.x.gz 200 200 1
trajout fuera restart
center :1-8 mass origin
image origin center
center :1-16 mass origin
image origin center
go

To recover the correctly imaged coordinates from the previous run and then
I pasted the velocities in this restart file...and the MD didn't give me
any problems...
am I doing correctly???
is there anyway to avoid this from happening in MD simulations using
sander??

my input file is :
title
 &cntrl
       irest=1, ntx=7,
       ntf=3, ntb=2, scee=1.2, cut=8.0,
       ntwx=500, ntwe=500,ntpr=500,
       nstlim=100000, dt=0.002,iwrap=1,
       temp0=300.0, ntt=1,
       ntp=1,
       ntc=3,

Thanks for your time

----------------------------------------------------------------
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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