Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

2014-10-19 Thread Wade
we deal with the drift when we use an affordable time-step in a long-time simulation? With best wishes, Wade ‍ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromac

Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

2014-10-18 Thread Wade
why does the conserved En. drifted with a constant rate in a 10 ns ?simulation for a pure water box (216 tip4p water)? With best wishes, Wade (part of the code please see below, I hope I have got the key point). ? ~~~

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 126, Issue 66

2014-10-18 Thread Wade
why does the conserved En. drifted with a constant rate in a 10 ns ‍simulation for a pure water box (216 tip4p water)? With best wishes, Wade (part of the code please see below, I hope I have got the key point). ‍ ~~~

[gmx-users] Conserved energy ("Conserved En.") in NVT simulation

2014-10-14 Thread Wade
Dear Mark and ALL, I am trying to calculate the conserved energy (H-tilde) in Bussi's stochastic velocity rescale algorithm (jcp,2007). In previous maillist, ‍Mark had mentioned that the conserved En. in ener file is the H in bussi's paper (http://permalink.gmane.org/gmane.science.biology.gro