From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Feb 12 2014 - 17:51:13 CST
I'll go one better. At the link below I've put together a demonstration simulation. It's based on the ATPase benchmark, and the only thing I've done is moved the OD1 atom on ASN33 of segname PSLN by roughly 0.2A.
- Untar into a directory of your choice
- load f1wations_xplor.psf / f1wations-pme-nve-200ps_PSLN_33_OD1_moved.pdb in VMD
- visualise "segname PSLN and resid 33" and "same residue as within 10 of (segname PSLN and resid 33)" in your choice of representation, and center your view on the former
- run namd using the config file f1atpase.namd
- In VMD, go to Extensions/Simulation/IMD Connect
- enter "localhost" in the Hostname box and 2030 in the Port box
- after allowing some time for the simulation to set itself up, click Connect
- enjoy (?) the show.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Bennion, Brian
Sent: Thursday, 13 February 2014 2:57 AM
Subject: namd-l: RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations)
In one of you posts you showed a histidine oscillating. can this be replicated with any histidine in your autoimd tests?
Does the asp need to be in the center of the box to be show the behaviour?
Would you mind posting your autoimd config files and I will have a go at it
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