主月 ：） wrote: > Hi: > Two things, > > - maybe you need a larger systems > - maybe g_gyrate does not take periodicity into account correctly. > extract some single molecules and look at them in a viewer, or write > your own script to compute Rg. > - have you used pbc = full for the simulations? > > 1.*The cell length about my PVME model is 4.5 nm which is big enough for > a PVME chain possesses all trans conformation.*
Fine, that would be a minimum necessary condition for something that was expected to extend fully. You should actually increase that so that in such a case the opposite ends can't see each other. You need margins at least as large as your largest cut-offs. You can see if this is a potential problem by seeing if any of your monomers do extend in this way. Your experimental system probably had room for about 10^8 such chains end to end, so there is a chance you're comparing apples and oranges here. > *2. The Rg is anaylzed by my own program, which has been validated.* > ** > *3.PBC=XYZ* Has this force field been demonstrated to be effective for this sort of simulation? If not, maybe you've begun to demonstrate that it isn't? Mark _______________________________________________ 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
