On Tuesday 10 June 2008 16:07, Mark Abraham wrote: > Peyman Yamin wrote: > > Good day! > > > > Thanks for the comments, but maybe it could be done in a less laborious > > way as following? > > > > g_energy gives all the interactions between MOL and SOL other than > > bonding ones. since there is no bond between MOL and SOL, one could do a > > ONE step simulation of MOL with its last acquired structure from solvent > > in vacuum and - since it's the whole system now - use g_energy again to > > get Angle and Dihedral energies. The only problem would then be the Bond > > itself (stretching) which is not important since when the MOL itself is > > the whole system, one could even use the tot-energy directly from the > > one-step MD in vac and by substracting get even the stretching energy. > > That seems at least roughly equivalent. Laborious is a subjective > judgement and depends what technique you would use to do it :-)
The world is subjective, to a great extent! ;) > > > should this be at least OK in a qualitative way. (?) > > > > Despite of a good discussion on the topic (march,2008 - David, Xavier, > > Pascal, Berk), I still can't find what contributes exactly to SR,LR and > > 1-4 non-bonding interactions and what does not, other that what they > > stand for ;) > > I said last time that the place to look for how these might be working > was in the early chapters of the GROMACS manual. The .mdp options you're > actually using will vary the manner in which these are calculated. > I know I know, but honestly there is not that much detail there! I think I should look at the code! and it's what I mostly try to avoid! But gmx is so nicely written that I've not done that since a long time - and become lazy! > > are they really independent and additive to give the whole interactions? > > Did you try adding them up? > Well yeah, and I get reasonable results! Qualitatively great! correlations are good, I have trends for interacions which are very good corresponding the other - not fully dependent - dynamic parameters, like those having a size feel - prediction of entropical trends for example, and their comparison with some simple theories gives beautiful results which make me xmgracing since some hours! > > or > > for example the Reaction Field corrections appliy to some and to some > > not? But as far as I FEEL, they are in a good way, so that one can do as > > above (at least with a reasonably small error). > > > > > > If it's not supposed to work from the beginning, i.e. the terms are not > > additive at all, please let me know! as well as if one should > > add/substract some things! > > First, try to understand the algorithm you're implementing. Then you > will have a much better idea what quantities are what. > It's true. I try to do this way mostly! Peyman > Mark > _______________________________________________ > 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 -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] _______________________________________________ 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
