PSF and PDB file for SWM4 water models

From: saman amiri (saman_amiri00_at_yahoo.com)
Date: Thu May 26 2011 - 07:37:04 CDT

• Next message: Jim Phillips: "Re: NAMD crashes when writing restart file and dcdfreq is 1"
• Previous message: Jim Phillips: "Re: Truncated octahedron box issues (?)"
• Next in thread: Jim Phillips: "Re: PSF and PDB file for SWM4 water models"
• Reply: Jim Phillips: "Re: PSF and PDB file for SWM4 water models"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi,

I am going to perform MD simulations using SWM4 water model. As mentioned before, NAMD Supports CHARMM Drude polarizable force field. However, there is no documentation regarding how to create PSF and PDB files for such a simulation. I used CHARMM toppar file "toppar_drude_master_c36a1.str " along with VMD to generate the PSF and PDB file but, it dose not work at all. The resulted files are not OK. Is there any comment about such a problem? Can someone please let me know how to deal with the problem.

Thanks,
Saman

• Next message: Jim Phillips: "Re: NAMD crashes when writing restart file and dcdfreq is 1"
• Previous message: Jim Phillips: "Re: Truncated octahedron box issues (?)"
• Next in thread: Jim Phillips: "Re: PSF and PDB file for SWM4 water models"
• Reply: Jim Phillips: "Re: PSF and PDB file for SWM4 water models"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:11 CST