I have tried using the soft core correction for values of lambda above 0.5, because i read that the overlaping starts usually at this lambda value. The problem is that now I values of deltaG where lambda is near 0.5 a little bit off-scale. What I mean is that what used to be a nice sequencial decrease in values from lambda 0 to lambda 1, now gives me a crazy value for lambda 0.5 (by crazy I mean 3 times larger) then for lambda 0.55, 0.6, 0.65 etc, I get values 3 times smaller than what they used to be. I guess that maybe using soft core correction for lambda values starting from 0.5 was a little bit to soon. But then for which lambda values should I start using soft core and how would I justify my choice? Thank you FabrÃcio Bracht
> I agree with Carsten. See perhaps the discussion at www.alchemistry.org as > well. > > On Fri, Aug 7, 2009 at 2:35 AM, Carsten Kutzner <ckut...@gwdg.de> wrote: > >> On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote: >> >> I am performing FEP do obtain the dimerization of a protein in >>> membrane. The lambda intervals i am using are 0.05 for each window. >>> After that I rerun each lambda .trr perturbing the system (plus)0.05 >>> and (minus)0.05 lambda value. Then with g-energy I obtain the deltaG >>> for each delta lambda. >>> Well, I have encountered a problem when trying to simulate the last >>> window (1.0 - 0.95 ). The simulation runs for a while and then dies. >>> The log file says >>> Step 2200 Warning: Pressure scaling more than 1%. >>> >>> Hi Fabricio, >> >> do you use soft-core? If not, I think you need to, at least for >> the intervals next to 0 and 1 to avoid singularities (these >> can result in undefined / NaN forces). See chap. 4.5.1 and >> 7.3.23 in the manual. >> >> Carsten >> _______________________________________________ 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/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
