AMBER Archive (2008)

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

From: dpandit_at_brandeis.edu
Date: Wed Jun 11 2008 - 13:17:56 CDT

Thank you, Nadia.

After investigating the issue, it seems there was a hidden glitch on
the server that affected the process. I will have to resubmit.

THX
Deepa

Quoting "Vahdati N." <nadiav_at_soton.ac.uk>:

> 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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