[gmx-users] pull code, lambda, and soft core availability
Upon further investigation, it appears that a soft core may help in this case. This is in spite of the fact that the problem is not a singularity, but that the dgdl term (dgdl=0.5*(Fc_B-Fc_A)*(r-r0)^2) gives very large values for Fc_A large enough to be significantly restraining and Fc_B = zero, where the sampling in the B state is massively unlikely to occur in the A state. I had originally thought that the lambda parameter would get included in dgdl (http://www.gromacs.org/pipermail/gmx-developers/2009-February/003004.html) but that is obviously not the case. I have found an alternative solution, but in case anyone else wants to follow this path in the future, it is possible that a lambda squared dependence would give improved behaviour since lambda would then be included in the dgdl equation. My quite possibly incorrect attempt at differentiation yields dgdl=(lambda-0.5)*Fc_A*(r-r0)^2 in this case where Fc_B=0.0, but in any event the (1-lambda)^2 term will ensure that lambda hangs around in some form, and this should reduce the uncertainties that occur near and at the no-restraint state. Chris. -- original message -- Thank you Matt, that is indeed the perfect paper. I'll post back here once I figure out exactly where the (1-lambda)^2 term would fit into the pull code US equation. Chris. This seems to be a good reference for soft-core interactions. BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. Chem Phys Lett (1994) vol. 222 pp. 529-539 On Thu, Feb 12, 2009 at 1:33 PM, wrote: Does anybody know of a good paper that describes the underlying equations that define soft core? Thanks, Chris. ___ gmx-users mailing listgmx-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
[gmx-users] pull code, lambda, and soft core availability
Thank you Matt, that is indeed the perfect paper. I'll post back here once I figure out exactly where the (1-lambda)^2 term would fit into the pull code US equation. Chris. This seems to be a good reference for soft-core interactions. BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. Chem Phys Lett (1994) vol. 222 pp. 529-539 On Thu, Feb 12, 2009 at 1:33 PM, wrote: Does anybody know of a good paper that describes the underlying equations that define soft core? Thanks, Chris. ___ gmx-users mailing listgmx-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
Re: [gmx-users] pull code, lambda, and soft core availability
This seems to be a good reference for soft-core interactions. BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. Chem Phys Lett (1994) vol. 222 pp. 529-539 On Thu, Feb 12, 2009 at 1:33 PM, wrote: Does anybody know of a good paper that > describes the underlying equations that define soft core? > > Thanks, > Chris. ___ gmx-users mailing listgmx-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
[gmx-users] pull code, lambda, and soft core availability
Hello, I see from looking at the source code that the free-energy lambda dependence is now available to the pull code based on pull_kB1. However, this leads to serious problems converging near lambda=1 when pull_k1=large and pull_kB1=0 and in the absence of a restraint (with k=0) the pulled COM is allowed to sample a large volume. I suspect that a soft core lambda dependence would help here, but the descriptions in the .mpd options section of the online manual indicate that this is available only for Lj and coulombic. Quoting: "sc_alpha: (0) the soft-core parameter, a value of 0 results in linear interpolation of the LJ and Coulomb interactions" Does anybody know if it is possible to get soft core potentials for an arbitrary coordinate? I tested the application of this myself by bypassing the free energy code and simply modifying the A-state pull_k1 value based on lambda 0->1 and then calculating dGdl from the px.xvg file myself. However, I am unclear how one would implement this as soft core. Does anybody know of a good paper that describes the underlying equations that define soft core? Thanks, Chris. ___ gmx-users mailing listgmx-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
