Hello Justin Sir, Greetings from Pawan. Sorry for the late reply. The max. force was 1.2447973e+o5 on atom 19448. This particular atom belongs to one of the lipid residues of the bilayer. I get Lincs warnings whenever I run the position restraint mdrun.
Thanking you, Pawan On Sat, Mar 21, 2009 at 6:08 PM, Justin A. Lemkul <[email protected]> wrote: > > > Pawan Kumar wrote: > >> Hello Justin Sir, >> >> Greetings from Pawan >> Thanks for your valuable suggestion and reply. >> Initially I gave the emtol of 1000 and the output I got was : >> Steepest Descents converged to machine precision in 163 steps but did not >> reach the requested Fmax<1000. >> Potential Energy = - 4.4516497e+05 >> >> > ...and how close did Fmax get to 1000? > > Even I tried to minimize the popc bilayer which I took from Tieleman sir's >> website ( before generating a bigger bilayer using genconf ) but that also >> converged to machine precision but not to the requested Fmax<1000. How do I >> proceed further ? >> > > Well, these things are not absolute; Fmax = 1000 is kind of a rule of thumb > that I use in my own work, but sometimes it is not necessary. Careful > equilibration should massage your system into cooperating. > > -Justin > > Thanks for your suggestions and help. >> >> Thanking you, >> Pawan >> >> On Thu, Mar 19, 2009 at 9:13 PM, >> >> Pawan Kumar wrote: >> > Hello Justin Sir, >> > >> > Greetings from Pawan >> > Thanks for your valuable suggestion and reply. >> > After inserting the protein in the bilayer using genbox I have >> minimized >> > the whole system without using any position restraints (i.e. define >> = >> > -DFLEXIBLE in em.mdp file). I used vanderwaal's distance parameter ( >> > -vdwd of 0.6 ) in the genbox step. >> > After running mdrun for energy minimization I got the output as : >> > Steepest Descents converged to Fmax<2250 in 14 steps. >> > Potential energy = - 6.9484700e+05 >> > Maximum force = 2.2114819e+03 on atom 34277 >> > Norm. of force = 5.0103039e+04 >> > >> >> You should try for an Fmax of no greater than 1000. 2250 is still >> very high. >> >> > I tried decreasing the emtol value in the em.mdp file but it >> ended with >> > machine precision. >> >> How far did it converge? What was Fmax? >> >> > I have read in literature that 5000 steps of Steetest Descents run >> is >> > required after inserting the protein in the bilayer which should be >> > followed by atleast 1000 steps of conjugate gradients. How can I >> > accomplish this ? Is there any parameter to be given in the >> em.mdp file >> > ? I use steep as the integrator in the mdp file for energy >> minimization. >> >> Read the manual. >> >> Whether or not that exact setup is going to be "required" is likely >> system-specific. I would say that as long as your system converges >> to a stable, >> negative Epot with a reasonable Fmax (less than 1000, but ideally >> lower) then >> you *may* have an appropriate starting structure. >> >> -Justin >> >> > Please help with some suggestions. >> > Thanks in advance. >> > >> > Thanking you, >> > Pawan >> > >> > >> > >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 > ICTAS Doctoral Scholar > 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 [email protected] > 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 [email protected] 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
