Re: About Usage of Topolgy and Parameter

From: Vidhya Sankar (vidhyasankar7928_at_yahoo.com)
Date: Mon Oct 14 2013 - 08:24:20 CDT

Dear sir,                Thank you for your Previous reply I am running the Namd Simulation After Energy Minimization It shows Very Popular error as follows ERROR: Constraint failure in RATTLE algorithm for atom 1242! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 1562! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 265! ERROR: Constraint failure; simulation has become unstable. ERROR: Exiting prematurely; see error messages above. Then I using VMD To get Namd plot (for total Energy)  It Shows the energy Suddenly falls to 7.5e+08  after 150 steps and Suddenly hikes  to 1.60e+09 at the end Em (1000steps) How to Solve it ? Which Parameter Should I Adjust ? Should I Diagnosis The Particular atom ? then i How to Diagnosis? Thanks in Advance On Monday, 14 October 2013 10:58 AM, Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu> wrote: Your message contains too little information to make any useful comments. On 10/13/2013 07:59 AM, Vidhya Sankar wrote: > Dear Namd User Thank you for your Previous Replies >  I have Constructed  My Lipid/Cyclic Peptide System Using CharmmAll atom > _36 toplology  files > My question Is > > can I Use the Charmm27 parmeters for that During Simulation ,  I need to > Change Only Atom Type OSLP to OSL Which is equivalent to Phosphate Oxygen > in Lipid  ( I think So) > > When I  change the Atom Type The Simulation Is Running Successfully > > If I use Charmm 36 Parameters It shows the Lack OF Angle and Dihedral > Parameters. > > > Thanks In Advance

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:45 CST