On Thursday 31 July 2008 13:34, Justin A. Lemkul wrote: > Peyman Yamin wrote: > > On Wednesday 30 July 2008 12:58, David van der Spoel wrote: > >> Peyman Yamin wrote: > >> > Hello List! > >> > > >> > > >> > > >> > I use g_sas to calculate the solvent accessible surface area of some > >> > > >> > amphiphiles. g_sas gives the result as hydrophobic area! I'm > > > > wondering if > > > >> > the hydrophilic part is somehow not recognized, or these terms mean > >> > > >> > different things in g_sas context? For Triton, for instance, a big > >> > > >> > surface is hydrophilic, to my knowledge! > >> > >> xmgrace -nxy sas.xvg > > > > Thanks David, but what about other question marks?! > > > > What is hydrophilic area? is it the wetted or solvated or maybe area on > > which the solvent molecules are with less than a distance apart from > > surface, or something else? In Triton, the length of the part which is > > interacting in a hydrophilic way is bigger actually, but I see a result > > of g_sas telling me that hydrophobic area is ~50 times bigger!! > Hi Justin, Thanks for the comments,
> I believe g_sas decides hydrophobicity and hydrophilicity based on charge > (and thus altered with the -qmax flag), from the description in the manual > page. I could be wrong, so someone please correct me if you are more > familiar with the code. > > I think you are thinking of the area somewhat backwards. Just because part > of the molecule is interacting with the solvent does not make it > hydrophilic surface area. Hence why you can have hydrophobic surface area > - if, for example, an alkyl chain is protruding into bulk solution, it is > actually hydrophobic, but accessible to solvent. > I think I said " interacting in a hydrophilic way" and not just "interacting". I completely agree with you on the fact that atoms could be accessible to the solvent and still be hydrophobic. In the end a vacuum in the solvent is not that desirable, I believe. But I more or less mean "wettet" in the context of Physical Chemistry, particularly D. Chandler (Nature|Vol 437|29 Sep 2005). > And, from what I understand, Triton is actually primarily hydrophobic, so a > 50X greater hydrophobic surface area does not surprise me. > TritonX100 has a big head which consists of a chain of ...-CH2-O-CH2-O-... . This (C2H4O)n , n~10 is actually hydrophilic and is bigger than the hydrophobic tail of the surfactant which is a 4-(1,1,3,3-tetramethylbutyl)-phenyl group. Based on this I expect the hydrophilic area should not be drastically smaller than the lipophilic part, as I get from g_sas. > > I use ffG43a1. Is it a strange behavior to calculate SAS from a UA > > > > trajectory? > > Not at all. I have seen such analysis in the literature. > > > I mean is the CHx groups' H size taken intro account ? > > > > > > > > How is the DGsolv calculated by g_sas? and the areas ? which algorithm? > > > > where is the code? reference? > > The code would be in g_sas.c, would be my guess. Have you - anyone else? - by chance seen any literature refering to the algorithm used in g_sas?? > > > Is there any program with which one could calculate the volume enclosed > > > > by SAS resulted from g_sas? Just if one used such and can trust any code > > > > available anywhere?? > > Volumes and densities can be printed with g_sas -tv, but I don't know if > this is what you're after. Well, this would be nice but I don't even have such a switch in my g_sas!! ------------------------------------------------------- Program g_sas, VERSION 3.3.1 Source code file: statutil.c, line: 799 Invalid command line argument: -tv ------------------------------------------------------- Peyman > > -Justin > > > I see different posts in the mailing list addressing the accuracy of > > > > g_sas! Well, I'm using gmx 3.3.1; is the accompanying g_sas reliable? > > > > > > > > Any comment is truthfully appreciated :) > > > > > > > > Peyman > > > >> P.S. Edmund Husserl believed, that we would indeed be in a nasty > >> > >> position, if empirical science were the only kind of science possible. > > > > -- > > > > 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 -- 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
