[gmx-users] pull code, lambda, and soft core availability

2009-02-12 Thread chris . neale
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

Re: [gmx-users] pull code, lambda, and soft core availability

2009-02-12 Thread Matt Wyczalkowski
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, chris.ne...@utoronto.ca wrote:

[gmx-users] pull code, lambda, and soft core availability

2009-02-12 Thread chris . neale
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