Hi Floris. So what you mean is that I should either use soft core for the entire transformation or not use it at all. But then I do not understand what Carsten said about using at least on lambda values close to 0 and 1. I thought that if I used soft core on the last point of my transformation (the one that crashed before I used soft core) I would eliminate the singularities produced by the end points. I got a little confused now. Thank you
> Hi Fabricio, > > It's not correct to change your value of alpha, you should use a single value > for the whole transformation. The soft core potential is constructed so that > the end points at lambda=0 and 1 represent the 'native' states (with no > influence from the soft core parameters), and that intermediate values > produce a smooth transformation. > Best, > > Floris > > > ________________________________ > From: Ragnarok sdf <fabrac...@gmail.com> > To: gmx-users@gromacs.org > Sent: Monday, 10 August, 2009 20:54:35 > Subject: [gmx-users] Re: Re: FEP problem with lambda perturbation 1 to 0.95 > > 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 > Fabrэcio Bracht > - Ocultar texto das mensagens anteriores - > >> 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
