>Message: 1 >Date: Tue, 21 Mar 2006 18:44:25 +0100 >From: Florian Haberl <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Re: Re:double precision minimization with > version 3.3 >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="utf-8" > >Hi, > >On Tuesday 21 March 2006 18:11, Yechun Xu wrote: >> Dear gmx users, >> >> First, I'd like to thank David's suggestion. It is not a bug of the >> program but a problem of installation. Now it is fixed and works fine. >> >> I met another problem about the double precision minimization (used for >> NMA later) with l-bfgs in version 3.3. It seems the optimization will never >> finish. The protein only includes 604 atoms (in vacuum) and the >> optimization started almost three weeks ago but only reach something like: >> "Step 29403607, Epot=-3.927499e+03, Fnorm=2.169e-01, Fmax=1.699e+00 (atom >> 451)" >> >> So my question is that the l-bfgs optimization does take very long time or >> there is some problem with my mdps file? Any suggestions are very >> appreciated! >> >> cpp = /lib/cpp >> define = -DFLEXIBLE >> constraints = none >> integrator = l-bfgs >> nsteps = 50000000 >> ; >> ; Energy minimizing stuff >> ; >> emtol = 0.000000001 >> emstep = 0.000000001 > >Your step size is too small > >standard are here (see handbook chapter 7.3): > >emtol = 100.0 [KJ/(mol nm)] >emstep = 0.01 [nm] > >so try this and if it doesn`t work, change the standard parameters with factor >10 or 100. >
> >Greetings, > >Florian > >-- >------------------------------------------------------------------------------- > Florian Haberl > Computer-Chemie-Centrum > Universitaet Erlangen/ Nuernberg > Naegelsbachstr 25 > D-91052 Erlangen > Mailto: florian.haberl AT chemie.uni-erlangen.de >------------------------------------------------------------------------------- > Thanks, Florian! But the optimization is not for MD but for NMA. So the emtol have to be 10-6 at least. Best regards Yechun _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
