Do you have water ? -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nicolas Sapay Sent: 2008年11月12日 4:15 To: Discussion list for GROMACS users Subject: Re: [gmx-users] the temperature effect in the simulation
He, Yang wrote: > Hi all users, > > When I change the temperature to try to get different disassociation about > the two DNA's strands. But even I change the value of temperature by 0K in > the mdp file , > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > Tcoupl = berendsen > ; Groups to couple separately > tc-grps = System > ; Time constant (ps) and reference temperature (K) > tau_t = 0.001 > The coupling constant sounds a bit small. The dynamics of fast motions may be affected more than you want, but I'm not a specialist of DNA and I don't know if it's a problem in that particular case. > ref_t = 300 > This indicates that your target temperature is 300K not 0K > ; Pressure coupling > Pcoupl = no > Pcoupltype = isotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Random seed for Andersen thermostat > andersen_seed = 815131 > > It will also disassociate .It is strange. > > Can anyone of you tell me what is the reason for that? > > Thank you in advance. > > Yang > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php