AMBER Archive (2008)

Subject: AMBER: problem with cartesian restraints with NTP simulations

From: Barbault Florent (
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


Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
tel : (33) 01-57-27-88-50
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