From: Jian Liu (bay__gulf618_at_sina.com)
Date: Mon Oct 19 2009 - 01:45:24 CDT
Hello Roman and others paying attention to this problem:
I have ran into a same problem as yours.
My system was built in various modelling softwares,
and the charges in water moleclues was confused somewhere.
It returned to normal after be corrected.
Hoping can help you
--- Jian Liu Master-degree graduate candidate majoring in Molecular Modelling Department of Physical Chemistry \& Chemical Physics College of Chemistry, Chemical Engineering and Materials Science Soochow University Suzhou 215123, China ----- Original Message ----- From: Roman Petrenko <rpetrenko_at_gmail.com> To: NAMD list <namd-l_at_ks.uiuc.edu> Subject: namd-l: spontaneous system explosion after 2 ns of normal run Date: 2009-10-15 11:57:34 Dear namd-ers, i simulated a protein system inserted in membrane in a water box with ions (total charge is close to zero) with PBC. Box size 159x159x112 A. NPT ensemble with electric field (of 1 namdconf unit) perpendicular to membrane was applied. Simulation runs normally up to 1,000,000 steps (2 ns) with normal decrease in total energy, temperature and pressures correspond to target values. Only slight increase in water box (by a couple of angstroms) was observed. Then, during the following 1.4 ns the box size increases to 5190x5190x3650 A and visually everything explodes. In other runs with exactly the same system but 10 times smaller electric field 4.4 ns of simulations are as expected. Should it explode when 10 ns is reached? Has anyone observed system explosion _after_ the system is minimized and partially equilibrated? -- Roman Petrenko Physics Department University of Cincinnati
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:35 CST