Re: parameter format for REMD simulations

From: Neelanjana Sengupta (
Date: Thu Jun 10 2010 - 04:00:41 CDT

   Dear NAMD community,

> We are attempting to perform a replica exchange molecular dynamics (REMD)
> simulation with NAMD2.7b2. We started with the alanin folding example, using
> the *given* .psf, .pdb and the alanin.params file.
> After that, we generated a .psf using psfgen and CHARMM topology
> (top_all22_prot_cmap.inp), and attempted to rerun REMD in the same way
> (using namd_replica_server.tcl, replica_exchange.tcl, and spawn_namd.tcl)
> using par_all22_prot_cmap.inp. This time, however, the simulations did not
> run, and we get the foll. messages in each log file:
> par_all22_prot_cmap.inp
> LINE=**>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<*
> We are not sure how to get over this problem. Do we really need to change
> the formats in the parameter file to match that in alanin.params?
> We would appreciate some help in this regard.
> Thank and regards,
> Neelanjana Sengupta
> ps: The alanin.params file is attached with this email.

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