Multi-step MD in a single .conf file

From: Jun Zhang (
Date: Mon Jun 21 2010 - 19:02:22 CDT

Hello everyone:

 I am performing a multi-tep md, first contrain the protein
 and relax the water by running for 1ns, then switch on SMD
 running for 1ns. In my .conf file I wrote
 SMD off
 minimize 2000
 run 1000000
 SMD on
 SMDvel ..
 run 1000000
 However, when the NAMD arrived at SMD on, it failed:
  TCL: Setting parameter SMD to off
 FATAL ERROR: Setting parameter SMD from script failed!
 Does this mean I cannot do this in a single MD run and must
 continue another MD by .restart file? If not, how can I set
 this? Thank you in advance.
 Best Wishes!
 Jun Zhang
 Nankai University


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