Hello, I'm having a similar problem, i.e. inconsistency between forward and reverse free energy calculations, in changing the chirality of a dihedral. In my case it is unlikely that there is histeresis, given that I have a long simulation. Could you be more specific about the bug you're referring to, I checked the reported known bugs and didn't find anything that was likely to cause this strange results.
Thanks Diana Lousa Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa Av. da República – EAN, 2780-157 Oeiras PORTUGAL ---------- Forwarded message ---------- From: Justin A. Lemkul <[EMAIL PROTECTED]> Date: 2008/6/16 Subject: Re: [gmx-users] Re: forward and reverse free energy not consistant (Li Qiang) To: Discussion list for GROMACS users <gmx-users@gromacs.org> Which GMX version are you using? There's a known bug in version 3.3.1 that has been fixed in 3.3.3. -Justin friendli wrote: > > Hi, > > I use thermodynamics integration. The protocol is 1000step energy minimization, 20 ps bond-constraint MD, and then 200ps MD for collecting dgdl. > > thanks > > Qiang > > Gerrit Groenhof wrote: >> >> Looks like hysteresis. Do you do slow growth, or discrete FEP? >> >> Gerrit >> >> >> >>> Dear all Gmxers, >>> >>> I am calculating a mutation free energy from L<->A for a five AA peptides using G96 53a6 force field. >>> however, my dG_for and dG_rev is quite different. >>> dG_for(lambda=0.00) = - 9.9 kJ/mol >>> dG_rev(lambda=1.00) = 1.33 kJ/mol >>> >>> Is there anything wrong with setting up topologies? >>> >>> Here is the [atoms] part for morphed atoms. and I attached the full .top in the attachment. >>> For L->A: >>> [ atoms ] >>> 17 CH2 2 LEU CB 6 0 14.027 CH3 0 15.035; qtot 1 >>> 18 CH1 2 LEU CG 7 0 13.019 DUM 0 13.019; qtot 1 >>> 19 CH3 2 LEU CD1 7 0 15.035 DUM 0 15.035; qtot 1 >>> 20 CH3 2 LEU CD2 7 0 15.035 DUM 0 15.035; qtot 1 >>> >>> >>> For A->L : >>> [ atoms ] >>> 17 CH3 2 ALA CB 6 0 15.035 CH2 0 14.027; qtot 1 >>> 60 DUM 6 DUM DUM 24 0 13.019 CH1 0 13.019 >>> 61 DUM 6 DUM DUM 24 0 15.035 CH3 0 15.035 >>> 62 DUM 6 DUM DUM 24 0 15.035 CH3 0 15.035 >>> >>> thanks for help >>> >>> LQ >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: topol_A2L.top >>> Type: application/x-extension-top >>> Size: 15230 bytes >>> Desc: not available >>> Url : http://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_A2L.bin >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: topol_L2A.top >>> Type: application/x-extension-top >>> Size: 15189 bytes >>> Desc: not available >>> Url : http://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_L2A.bin >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> gmx-users mailing list >>> gmx-users@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before posting! >>> >>> End of gmx-users Digest, Vol 50, Issue 50 >>> ***************************************** >>> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 >> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > -- ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
