Regarding Production Run in NAMD

From: amit banerjee (amit_informatics_at_yahoo.com)
Date: Wed Jul 10 2013 - 00:14:34 CDT

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Dear All,                 I am interested in performing a simple simulation of a protein molecule in water in a cube box. But as per NAMD protocol or the User Guide no mention is there for production run similar to GROMACS or AMBER. Can anyone help me out in this regard with the production run tcl script file (if at required in NAMD). Few questions i want to clarify in this regard: 1. If separate production run TCL script is not required how to complete the MD simulation? 2. For SMD simulation the specified requrement is performing equilibriation in a cube box, is it possible to do the SMD after equilibriating in a sphere?   Looking forward for your support and suggestions.   Best regards,   Amit Kumar IICT, India.

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