----- Original Message ----- From: "Justin A. Lemkul" <jalem...@vt.edu> Date: Sunday, May 23, 2010 13:49 Subject: Re: [gmx-users] xtc file To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> > > Moeed wrote: > >Dear experts, > > > >I am trying to exclude all nonbonded interaction on hexane molecule. > > > > > >1-For the md -rerun command I do not know how to get the input > XTC file. the program is expecting rerun.xtc > > > >mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o > ORIGINAL-Trajectory-NOexcl.tpr* -c Hexane-Stack125_after_md -v > >& output.mdrun_m > > > > As I think I have said several times, you have to do this in > several steps. First, run a simulation using normal exclusions > that you believe to be valid by evaluating the properties of the > system. If you set nstxtcout > 0 in your .mdp file, you > will get a .xtc trajectory file (.xtc output is off by default - > you must specify that you want it). After you have done > this, use mdrun -rerun on this trajectory and whatever modified > topology you have created. More precisely, mdrun -rerun will take any trajectory file, as can be seen by inspecting mdrun -h. There is no need to create an XTC file. There is a need to tell the previous mdrun to write positions when you want them to be available for the rerun, either with nstxout or nstxtcout. > More specifically: > > 1. mdrun -deffnm md_no_excl > 2. grompp to create new .tpr file with special exclusions > 3. mdrun -rerun md_no_excl.xtc -s md_with_new_excl.tpr > > Thus, new energies will be calculated from a sensible trajectory. > > >2-Can you please check exclsusions directive in top file. I > have used also nrexcl 5 in molecule top. does this make sense > given that I have defined all the possible exclusions in 19 lines. > > > > Much of what you have defined is redundant. If you have > nrexcl = 5 that means nonbonded interactions between atoms up to > 5 bonds away are excluded already, so lines like "19 20" are > unnecessary. Yep, use one approach or the other. Both won't hurt, but are redundant and error-prone. Mark > <snip> > > All of the information I deleted is unnecessary. I > appreciate that you are trying to be thorough, but long emails > with excess detail dilute the information that is really needed. > > >[ moleculetype ] > >; > Name nrexcl > >Hexane 5 > > > > Not a bad approach, but... > > >[ exclusions ] > >1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > >2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > >3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > >4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > >5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > >6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > >7 8 9 10 11 12 13 14 15 16 17 18 19 20 > >8 9 10 11 12 13 14 15 16 17 18 19 20 > >9 10 11 12 13 14 15 16 17 18 19 20 > >10 11 12 13 14 15 16 17 18 19 20 > >11 12 13 14 15 16 17 18 19 20 > >12 13 14 15 16 17 18 19 20 > >13 14 15 16 17 18 19 20 > >14 15 16 17 18 19 20 > >15 16 17 18 19 20 > >16 17 18 19 20 > >17 18 19 20 > >18 19 20 > >19 20 > > > > > ...why all the redundancy? Much of what you have here is > already encompassed by the value of nrexcl. Actually, if > you set nrexcl = 7, you don't have to create an [exclusions] > section at all! There are no atoms more than 7 bonds away > from each other in hexane, right? > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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://lists.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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.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
