Hi Po-chia, On Sep 10, 2013, at 9:53 AM, "Chen, Po-chia" <pc...@gwdg.de> wrote:
> Hi all, > I can't seem to find the correct combination of EDI parameters impose a > harmonically-constrained simulation along an eigenvector in GROMACS 4.6.2, > and I'd like to confirm that the inputs I have are actually correct. Here is > the make_edi command I used to generate the .edi file fed to mdrun: > > echo "C-alpha System" | make_edi -restrain -harmonic \ > -f ../ca-evec.trr \ > -eig ../ca-eval.xvg \ > -s ../analysis.tpr \ > -ori ./init.gro \ > -outfrq 2500 -deltaF0 150 -Eflnull 100 -flood 1 \ > -o constrain.edi I think you should add -tau 0 when using flooding as harmonic restraint (since you do not want the flooding potential to change). > Where the eigenvectors and eigenvalues are previously derived by g_covar for > a set of unrestrained trajectories. The origin file init.gro is the same as > the starting coordinates of this constrained run, extracted from a previous > EDI run to start at an appropriate location on the eigenvector space. > > The 1st eigenvalue is ~ 66, and the eigenvector looked fine in VMD when > plotted by g_anaeig -extr. > > So mdrun -ei constrain.edi runs normally, but the flooding potential drops to > zero so the protein diffuses freely along the 1st eigenvector. e.g. the > first/last line in edsam.xvg looks like: > # time RMSD EV1projFLOOD EV1-Ef1 EV1-Vf1 EV1-deltaF > 0.0 0.43 9.99 -9.4e+1 9.5e-8 3.8e-9 -5.3e-4 > 10.0 0.40 9.49 0.0 -0.0 1.6e-44 -0.0 > ... > 10000.00 0.94 -2.2 0.0 -0.0 1.6e-44 -0.0 > > When c(0) is supposed to be according 9.99 as I set init.gro to be the -ori. > Do I need to change -alpha as well? What parameters am I missing/added by > mistake? The manual gives no indication as to which ones to do. Can you check whether make_edi -ori wrote the correct position on the 1st eigenvector in your .edi file? Scroll down to a line called # NUMBER OF EIGENVECTORS + COMPONENTS GROUP 7 (Group 7 means the flooding vectors), if you have a single flooding vector, the next line should read "1" and in the following line you will find three entries that describe <nr> <spring constant> <reference projection> <ref. proj. change per time step> which I guess read in your case 1 1 9.99 <no 4th entry> so the reference projection should be 9.99, as calculated from your .ori structure. If there is no 3rd entry, you can simply put it there manually (and leave away the -ori option to make_edi). Best, Carsten > > = = = > P.S. the relevant constrain.edi lines contain: > ... > #DELTA_F0 > 150.00 > #INIT_DELTA_F > 0.0 > #TAU > 0.10 > #EFL_NULL > -100.00 > #ALPHA2 > -1.0 > #KT > 2.50 > #HARMONIC > 1 > #CONST_FORCE_FLOODING > 0 > ... > -- > 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/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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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/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