On Saturday, March 23, 2013, Shima Arasteh wrote: > That's right. > But I' d like to be sure about this fact that both restraints are applied. > I see just 1 position restraints energy term in log file. Is just > visualizing the trr file the only way of becoming sure that the headgroups > and protein are restrained? > > > Either that or by measuring coordinates over time with g_traj. Effects of restraints should be fairly obvious when visualized.
And one more question is that, to eliminating the position restraints in > MDRUN, is it supposed to reduce the force on atoms before mdrun gradually? > Or it is ok to reduce it in MD step? > > I am not sure I understand what you are asking. It is usually sufficient to simply turn off the restraints, but some people like to do a gradual release. I usually do not find that necessary. -Justin > Thanks for your suggestions. > > > Sincerely, > Shima > > > ----- Original Message ----- > From: Justin Lemkul <[email protected] <javascript:;>> > To: Shima Arasteh <[email protected] <javascript:;>>; > Discussion list for GROMACS users <[email protected] <javascript:;>> > Cc: > Sent: Saturday, March 23, 2013 10:37 PM > Subject: Re: [gmx-users] define statement in mdp file > > > > On 3/23/13 8:59 AM, Shima Arasteh wrote: > > Hi, > > > > I need to set position restraints on phosphorus head groups of lipids in > addition of protein. > > > > In mdp file I added two lines: > > define = -DPOSRES > > define= -DPOSRES_LIPID > > > > But I get the error that multiple define assignments are not allowed. Is > the "define= -DPOSRES_LIPID" is enough for both protein and headgroups? > > > > Not likely, but that depends on the construction of your .top. I will > assume > that each #define statement controls a separate topology, which is a good > idea. > > The correct approach is to specify as many define statements as you like > on one > line (this is really just stolen from cpp): > > define = -DPOSRES -DPOSRES_LIPID > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
