AMBER Archive (2008)

Subject: RE: AMBER: Equilibration/Heating - Protein fixed -Problem

From: Vahdati N. (nadiav_at_soton.ac.uk)
Date: Wed Jun 11 2008 - 12:38:50 CDT


Hi,
Did you have a time limit on the run-time? It could be that you have just not set the run-time for long enough.
Nadia

________________________________________
From: owner-amber_at_scripps.edu [owner-amber_at_scripps.edu] On Behalf Of dpandit_at_brandeis.edu [dpandit_at_brandeis.edu]
Sent: 11 June 2008 16:31
To: amber_at_scripps.edu
Subject: AMBER: Equilibration/Heating - Protein fixed -Problem

Hi Amber Community:
                    I am trying to perform initial
heating/equilibration for 40 PS keeping the protein restrained. My
protein is a dimer. Based on past emails, I have set tempi = 150 K and
temp0 = 310 K and I am using Langevin dynamics for temperature
regulation. It seems to me my job is not fully done. Please find the
attached output file for details. I am unable to find which parameter
might have caused the problem.

THX
Deepa

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