Yep, all atoms begin to freeze....even the ones not being perturbed (i.e. the water molecules). It's pretty strange. It only happens for lambda=1.0. Below is my .mdp file.
; Run Control integrator = md ; calculation type dt = 0.0015 ; time step (ps) emstep = 0.1 ; step size for steepest descent (nm) nsteps = 3000000 ; number of steps gen_vel = no ; velocity generation on startup comm_mode = linear ; center of mass restrictions nstcomm = 100 ; center of mass motion removal frequency ; Free Energy Perturbation free_energy = yes init_lambda = 1.0 delta_lambda = 0 sc_alpha = 0.5 sc_power = 1 sc_sigma = 0.3 ; Data Output Options nstxout = 5000 ; coordinate output frequency nstvout = 5000 ; velocity output frequency nstlog = 5000 ; energy output frequency to log file nstenergy = 5000 ; energy output frequency to energy file ; Neighbor-list nstlist = 15 ; neighbor-list update frequency ns_type = grid ; type of neighbor-list pbc = full ; periodic boundary conditions ; Cut-off distances rlist = 1.2 ; cut-off distance for neighbor-list (nm) rvdw = 1.2 ; cut-off distance for vdw (nm) rcoulomb = 1.2 ; cut-off distance for coulomb (nm) dispcorr = EnerPres ; Electrostatics coulombtype = PME ; electrostatics method pme_order = 4 ; interpolation order of PME optimize_fft = yes ; optimization of FFT grid at startup fourierspacing = 0.12 ; grid spacing (nm) On Jan 22, 2008 3:45 AM, Maik Goette <[EMAIL PROTECTED]> wrote: > Do really all atoms "freeze". So also the atoms, which are not perturbed? > Can you post your mdp-file? > > > Regards > > Maik Goette, Dipl. Biol. > Max Planck Institute for Biophysical Chemistry > Theoretical & computational biophysics department > Am Fassberg 11 > 37077 Goettingen > Germany > Tel. : ++49 551 201 2310 > Fax : ++49 551 201 2302 > Email : mgoette[at]mpi-bpc.mpg.de > mgoette2[at]gwdg.de > WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > > > Robert Johnson wrote: > > The distortion was occuring because my position restraint potential > > was too weak. Increasing the force constant keeps the base in the > > right conformation. > > > > I believe my topology is correct, but it seems that turning off the > > VdW parameters causes the base to distort. I will look into this more. > > > > Also, even with sc_alpha=0.5, I'm still experiencing this weird > > "freezing" when lambda=1.0. The trajectory proceeds normally for about > > 2.1 ns, then all of a sudden all motion freezes and the atoms simply > > vibrate about their "equilibrium positions". Any other ideas what > > might cause this? > > Thanks, > > Bob > > > > On Jan 21, 2008 3:39 AM, Maik Goette <[EMAIL PROTECTED]> wrote: > >> Robert > >> > >> A value for alpha of 0.5 should work, although I tested some different > >> alphas with different test systems and I have to say, that a proper > >> value can be between 0.2 and 0.7 depending on the system itself. > >> The distortion, you describe is really strange. I calculated DNA and > >> single bases a lot and never saw something like that. Even a fully > >> "dummy-base" is stable, if your topology is correct. The bonded terms > >> are sufficient to keep it in the right conformation. > >> Are you sure, your position restrains in the topology are used with the > >> correct structure file? > >> > >> Maybe, I should also mention, that, especially with such large > >> perturbations as a full DNA-base, you should split your topology into 2, > >> where you switch off the QQ hardcore and the VdW softcore in two steps. > >> > >> Regards > >> > >> Maik Goette, Dipl. Biol. > >> Max Planck Institute for Biophysical Chemistry > >> Theoretical & computational biophysics department > >> Am Fassberg 11 > >> 37077 Goettingen > >> Germany > >> Tel. : ++49 551 201 2310 > >> Fax : ++49 551 201 2302 > >> Email : mgoette[at]mpi-bpc.mpg.de > >> mgoette2[at]gwdg.de > >> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > >> > >> > >> Robert Johnson wrote: > >> > >>> Thank you David and Maik for your detailed replies. Yes, I am trying > >>> to obtain an absolute free energy of binding. My thermodynamic cycle > >>> is: > >>> > >>> NT+DNA(adsorbed) -> NT+ DNA(desorbed) (obviously this is not the one > >>> that I'm obtaining with the alchemic method) > >>> > >>> Thus, the one I'm using in the simulation is: > >>> > >>> Water + NT + DNA(adsorbed) -> Water + NT + nothing (DNA dissapears) > >>> Water + DNA -> Water + nothing > >>> > >>> Any suggestions about this? I will check out your recent publications. > >>> > >>> I believe my topology is properly formatted. I wasn't expecting the > >>> large distortions because I was using position restraints. Thus, I was > >>> expecting the base to remain in about the same geometry. Perhaps I > >>> will increase the force constant for the restraining potential. > >>> > >>> I am going to repeat some of these computations using sc_alpha=0.5. > >>> > >>> Thanks for your help. > >>> Bob > >>> > >>> On Jan 17, 2008 2:24 PM, David Mobley <[EMAIL PROTECTED]> wrote: > >>>> Robert, > >>>> > >>>>> I'm computing the free energy of binding of a DNA base on a carbon > >>>>> nanotube. I think it's a pretty simple calculation and I'm proceeding > >>>>> in a very standard way. This is what I'm doing: > >>>> An absolute free energy? This isn't necessarily straightforward -- > >>>> there are a lot of wrinkles. Some of my recent work has some > >>>> discussions if this if it's helpful. > >>>> > >>>>> I have the optimal orientation of the base on the nanotube. I'm > >>>>> constraining the positions of the base atoms with a soft harmonic > >>>>> potential. > >>>> OK, that's a good idea for standard state reasons (see the 2003 > >>>> Boresch paper) among other things. > >>>> > >>>>> I then am running two different FEP calculations: one where I turn off > >>>>> the charges on the base atoms and a second where I then turn off all > >>>>> the lennard-jones parameters for the base atoms. For each of these I > >>>>> use the following: > >>>>> delta_lambda = 0 > >>>>> sc_alpha = 0.7 > >>>>> sc_power = 1 > >>>>> sc_sigma = 0.3 > >>>>> > >>>>> I run a series of trajectories at constant lambda values from 0 to 1. > >>>> OK. I have some information posted on what I think the best settings > >>>> are for these on alchemistry.org, especially at > >>>> http://www.alchemistry.org/wiki/index.php/Best_Practices. It is still > >>>> in progress but may be somewhat helpful. I doubt this is the source of > >>>> your problems though, although I prefer a sc_alpha = 0.5 which may > >>>> improve the situation somewhat. > >>>> > >>>>> However, I notice some problems with the trajectories when I turn off > >>>>> the LJ parameters. As lambda is varied from 0 to 1, it seems that the > >>>>> position restraints no longer are being applied. Additionally, the DNA > >>>>> base geometry starts to become severely distorted at lambda values > >>>>> greater than about 0.6. This happens despite the fact that I am not > >>>>> perturbing the internal bonded interactions of the base. Here is a > >>>>> sample of my topology (included just the first line of each section): > >>>> Hm, on the position restraints, depending on your version of gromacs > >>>> you may need to additionally specifiy the B state position restraints, > >>>> else these may be assumed to be zero. I believe you can do this by > >>>> adding additional columns in your posre.itp that give the B state > >>>> parameters. > >>>> > >>>> In terms of distortion, it's not clear to me why you think the > >>>> molecule should *not* be distorted once you turn off the LJ > >>>> interactions (which includes internal LJ interactions). The bonded > >>>> parameters (especially torsions) are of course derived after LJ > >>>> parameters are already fitted, in most cases, so they only can be > >>>> relied on to give meaningful conformations when the LJ interactions > >>>> are on. The beauty of the thermodynamic cycle approach, though, is > >>>> that you can (at least in principle) get correct binding free energies > >>>> even if your molecule of interest samples wacky, artificial > >>>> conformations when it's noninteracting. > >>>> > >>>>> Also, I am experiencing additional problems when lambda=1. After about > >>>>> 2ns, all the motion in the system begins to freeze and all the atoms > >>>>> simply vibrate about a fixed position. Soon after that the simulation > >>>>> crashes. > >>>> My experience has been that sc-alpha = 0.7 can lead to a fairly steep > >>>> dV/dlambda and some large forces near lambda=1, which is why I > >>>> recommend sc-alpha = 0.5. This parameter is actually fairly sensitive. > >>>> This *could* lead to crashes, but I don't know about > >>>> freezing/vibrating. > >>>> > >>>> Let me know if this helps. > >>>> > >>>> Best wishes, > >>>> David Mobley > >>>> UCSF > >>>> http://www.dillgroup.ucsf.edu/~dmobley > >>>> > >>>>> Can anyone comment on what's going on here? > >>>>> Thanks, > >>>>> Bob Johnson > >>>>> _______________________________________________ > >>>>> 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 [EMAIL PROTECTED] > >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>>>> > >>>> _______________________________________________ > >>>> 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 [EMAIL PROTECTED] > >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>>> > >>> _______________________________________________ > >>> 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 [EMAIL PROTECTED] > >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>> > >>> . > >>> > >> _______________________________________________ > >> 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 [EMAIL PROTECTED] > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > _______________________________________________ > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > . > > > _______________________________________________ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
