AMBER Archive (2008)

Subject: AMBER: problem with cartesian restraints with NTP simulations

From: Barbault Florent (florent.barbault_at_univ-paris-diderot.fr)
Date: Wed Nov 19 2008 - 08:50:13 CST

Dear Amber users,

I am facing a problem with restraints on Amber 9. I am using cartesian
restraints (ntr=1) with this sort of mask:

restraintmask = '(:112 >@8.0) :1-111!@H'

I tried to do some MD with this sort of restraint in explicit solvent.
Generally, I share my simulation in several runs (generaly 100ps). When I do
these simulations in NVT I have no problem (ntb=1). However, if I launch the
same simulation in NTP, my restraint energy always begins with a huge value
on every starting runs. I don't have this problem if I don't share my
trajectory into several runs. Therefore, I think my problem arises from the
reading of coordinates when the non-bonded atom list is created. Is there any
people who have an idea how to solve my problem?

Best regards
Florent Barbault

-------------------------------------------------
Dr Florent Barbault
Maitre de conferences

NEW ADDRESS !!!

Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
http://www.itodys.univ-paris7.fr/
tel : (33) 01-57-27-88-50
e-mail : florent.barbault_at_univ-paris-diderot.fr
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