From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jan 08 2009 - 10:58:05 CST
On Thu, 8 Jan 2009, Do Nhu Trang wrote:
DNT> Dear all,
DNT> I would like to perform a simulation with restraints released gradually. I
DNT> want to control several phases in one configuration file. The procedure I
if i remeber correctly, NAMD doesn't handle this scenario very
gracefully. you better be using multiple input files. there is
next to no gain from having this in one script anyways.
DNT> have done is the following:
DNT> 1. turn on the constraints
DNT> 2. specify the reference pdb file together with force constant
DNT> 3. run for a number of timesteps
DNT> 4. turn off the constraints
DNT> 5. turn on again with another reference pdb file and force constant
DNT> 6. run for another number of timesteps
DNT> The detail script of this part is attached below. After running for the
DNT> first number of steps (20000 in this case), NAMD stops running and reports
DNT> this following error:
DNT> "TCL: Setting parameter constraints to off
DNT> FATAL ERROR: Setting parameter constraints from script failed!"
DNT> I found the similar problem reported by Marc vander Kamp a long time ago
DNT> but there is still no reply to this message. I would like to ask Marc if he
DNT> could already solve this problem, and I also need help from all NAMD users.
DNT> Many thanks.
DNT> constraints on
DNT> consref K_18_restrained_5.pdb
DNT> conskfile K_18_restrained_5.pdb
DNT> conskcol B
DNT> run 20000;
DNT> constraints off;
DNT> constraints on;
DNT> consref K_18_restrained_3.pdb;
DNT> conskfile K_18_restrained_3.pdb;
DNT> conskcol B;
DNT> run 5000;
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:20 CST