Hi Justin, My box size is 3.13690 3.73000 2.70000 and I use the user-defined potential functions.
#define _FF_GROMACS #define _FF_GROMACS1 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 #include "ffyxhnb.itp" #include "ffyxhbon.itp" This is my ffyxh.itp file Also I have change the value of tau_t by 0.1 but it did not work. Please let me know if you need any further information. Thank you. Yang ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL PROTECTED] Sent: Tuesday, November 11, 2008 12:12 PM 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 > ref_t = 300 I don't know if this is relevant or not, but a coupling constant of 0.001 is exceptionally short. What is the timestep in your simulation? Typically one sees tau_t = 0.1 with a timestep of 0.001-0.002 ps. > ; 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. So the dissociation occurs at 0K and 300K? Sounds like something is fundamentally flawed with your system setup. How large is your box? What force field are you using? -Justin > > 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 > -- ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ 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