Respected Sir, Greetings from Pawan. Thanks for your reply. I used to do genbox first and then Inflategro all the time. Is it possible to concatenate one file after the other using " vi editor" - I mean just copying the contents of the membrane.gro file at the end of protein.gro file ? Is it fine if I generate the .gro files using editconf command ? Thanks for your kind help.
Thanking you, Pawan On Mon, Mar 23, 2009 at 5:02 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Pawan Kumar wrote: > >> Respected Sir, >> >> Greetings from Pawan. >> Thanks for your mail. >> I will tell you in detail. >> The control lipid bilayer ( which is generated using genconf -nbox 2 2 1 >> -dist 0 0 0 ) minimized fine with an emtol value of 1510. >> Then after inserting the protein with genbox the whole system minimized >> with an emtol value of 2250. >> Then I am trying to do position restraint mdrun where I am getting errors. >> Inflategro can be used only after inserting the protein right (which I did >> using genbox with -vdwd option as 0.6) ? >> >> > No. Read the documentation carefully. You first concatenate your protein > and membrane .gro files, then use InflateGRO on that system. There is no > genbox involved when using InflateGRO, hence why I suggested it as a > (potentially) more reliable method. > > -Justin > > Thanking you, >> Pawan >> >> On Mon, Mar 23, 2009 at 4:39 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Pawan Kumar wrote: >> >> Hello Justin Sir, >> >> Greetings from Pawan. >> Sorry for the inconvenience. >> Next time I will keep in mind about the subject line. >> I tried deleting those particular atoms where it gave the >> maximum force. >> >> >> You said that this atom was part of a lipid. Deleting these atoms >> will give you a broken structure and an unrealistic system. It >> should also cause grompp to complain. >> >> >> But every time a new atom with a maximum force was given in the >> output. >> Is it fine to use to use "constraints = all-angles" in order to >> overcome the Lincs warnings ? >> >> >> No. LINCS warnings indicate that there is something fundamentally >> wrong with your system. It likely stems from how you inserted your >> protein into the lipids. Think about it. Your control lipid >> bilayer minimized fine. Your protein-membrane system does not, if >> that is what we're still talking about. That indicates to me that >> the problem is not with the lipids, the problem is with the >> insertion of the protein. >> >> Instead of genbox (which is somewhat crude), try the InflateGRO >> script from Tieleman's site. I have used it many times to build >> nicely-packed membrane protein systems. It takes substantially >> longer to build the system than with genbox, but I think the results >> are more reliable. >> >> -Justin >> >> Thanks in advance. >> >> Thanking you, >> Pawan >> >> >> >> >> On Mon, Mar 23, 2009 at 4:16 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> When replying to digests, please change the subject line to >> something relevant. >> >> Pawan Kumar wrote: >> >> Hello Justin Sir, >> >> Greetings from Pawan. >> Sorry for the late reply. >> The max. force was 1.2447973e+o5 on atom 19448. >> >> >> An Fmax that high is sure to generate problems. It is up to >> you to >> inspect your system, understand which atoms are interacting >> to cause >> such a force, and determine if you've done something wrong. >> >> -Justin >> >> 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 >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> 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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org >> <mailto: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 >> gmx-users-requ...@gromacs.org <mailto: >> gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>>. >> 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 <http://vt.edu> <http://vt.edu> >> <http://vt.edu> | (540) >> >> 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org >> <mailto: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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>>. >> 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 <http://vt.edu> <http://vt.edu> | (540) >> 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> 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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> >> > -- > ======================================== > > 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 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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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