How long the MD simulation should be? The problem is that I run multiple simulation (a hundred at a time) and the MD are really time consuming. I should probably can't do it, if the time you propose is too long, I probably forget it.
Thank you -------------------------- Pierre THEVENET Ph.D. Candidate INSERM - MTi Ecole Doctorale B3MI Université Paris Diderot - Paris 7 2012/4/10 Justin A. Lemkul <jalem...@vt.edu> > > > pitheve...@free.fr wrote: > >> >> Here is what I have done: >> >> First, I created the .gro file with the command line: >> pdb2gmx -f test.pdb -o test.gro -p test.top -ignh -missing >> >> >> Then, I added at the end of my test.top file the following lines (I >> double checked the atom numbers): >> >> [ distance_restraints ] >> ; ai aj type index type' low up1 up2 fac >> 37 140 1 0 1 0.19 0.21 0.22 1 >> >> then, I done: >> editconf -f test.gro -o test-box.gro -d 2.0 -c -bt cubic >> >> grompp -c test-box.gro -p test.top -o test-min.tpr -f test-em.mdp >> >> mdrun -s test-min.tpr -c test-min.gro -deffnm test-min -v -nice 0 >> >> >> and finally get my new pdb file with: >> >> editconf -f test-min.gro -o test-min.pdb >> >> But it didn't seemed it had make the two sufur atom closer than if I >> didn't add the distance_restrain in the top file. >> >> Did I do something wrong? >> >> > Simple energy minimization is unlikely to give rise to the structural > changes you need to bring these atoms close together. Running a short MD > simulation may work, though if the atoms are very far apart and you force > them together quickly, you may have stability issues. > > > -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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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