It's like looking for a black cat in a dark room. If to multiply the result by 1000 (derived from units) and divide it by 3 - the resulting value seems to be close to the correct one.
Hope it's true. I will try to describe this tricky procedure in the gromacs wiki now. Vitaly On Fri, Mar 6, 2009 at 12:56 PM, Florian Dommert <[email protected]> wrote: > > Hi, > > > On 06.03.2009, at 12:37, "Vitaly V. Chaban" <[email protected]> wrote: > >> Hi, >> >> I checked the VACF calculation with the results obtained with my >> utility, it's completely correct with >> g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol >> where an.ndx contains all the number of atoms of the needed molecule. >> > sounds very good. In my opinion it is a question of units. After using > g_analyze you end up with nm^2 / ps very uncommon for a diffusion > coefficient. So if you convert this to more convenient units you should > obtain the expected value. > Cheers > Flo >> >> The problem is evidently in the integration. I suspect it's something >> with units there. >> >> Does >> g_analyze -integrate >> give a pure integral of the function supplied? '*1/3' is not performed >> (at least there is nothing about it in the manual)... >> >> Vitaly >> >>> Hi Flo, >> >>> Yes, I remember our talk about this problem about a year ago. >>> >>> So what should be the correct notation now? >>> >>> I just tried >>> g_velacc_402f -acflen 1001 -nonormalize -n an.ndx >>> or >>> g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol >>> and then g_analyze -integrate -f vac.xvg >>> >>> but they give me a value close to 0... >> > _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
