Perhaps a naive question, but which version of Gromacs are you using? Such issues are well-known in 3.3.1, but have been fixed in the most recent release (3.3.3).
-Justin Quoting Robert Johnson <[EMAIL PROTECTED]>: > Hi Maik, > That's exactly what I'm attempting to do...morph G to A etc. All I'm > doing here is turning off the charges of G and then turning them on > again. Wouldn't you do this anyway in the morph step? Wouldn't the > process go something like: Turn off charges -> Morph LJ parameters -> > Turn on charges. > > It seems like I've got to be doing something wrong. I can't believe > that simply turning off/on the charges would drastically perturb the > entire system and prevent convergence. > Bob > > > On Thu, May 8, 2008 at 6:12 AM, Maik Goette <[EMAIL PROTECTED]> wrote: > > Hi Robert > > > > Sounds familiar to me. I also tried to compute free energy differences by > > letting whole bases appear/disappear. I ran into the same problems and > > haven't found a solution yet. Probably the perturbation is too large to > gain > > converged results. My solution was stopping those simulations. > > This doesn't sound promising, I know, but actually, I fear, there is no > > proper solution. Maybe you should morph G to A or T to C or something like > > that, where just a few atoms have to be perturbed. > > > > Regards > > > > Maik Goette, Dipl. Biol. > > Max Planck Institute for Biophysical Chemistry > > Theoretical & computational biophysics department > > Am Fassberg 11 > > 37077 Goettingen > > Germany > > Tel. : ++49 551 201 2310 > > Fax : ++49 551 201 2302 > > Email : mgoette[at]mpi-bpc.mpg.de > > mgoette2[at]gwdg.de > > WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > > > > > > Robert Johnson wrote: > > > > > > > > > > > > > > Hello everyone, > > > I'm trying to calculate the free energy of binding of DNA bases on a > > > carbon nanotube. I'm running some tests to make sure that I'm doing > > > everything correctly. One thing I tried was turning off all the atom > > > charges of the DNA base and then turning them back on again. > > > Theoretically, the free energy changes of these two processes should > > > be equal and opposite and thus sum to zero. However, this is not what > > > I'm finding. > > > > > > For guanine, I get a free energy change of 648 kJ/mol and -618 kJ/mol > > > for turning off and turning on the charges, respectively. Obviously, > > > they are not equal by 30 kJ/mol, which seems pretty big. I have done > > > some error estimation using the g_analyze -ee program. One thing I > > > find strange is that the error estimates in dV/dl for TURNING ON the > > > charges is large (over 2) and do not even converge for a 7.5 ns > > > simulation. In contrast, the error in dV/dl for TURNING OFF the > > > charges converges extremely quickly (using small block sizes of 50 or > > > less) and is smaller at 0.3. So it seems like I have some sampling > > > problems with the TURNING ON portion. Is there some reason why you > > > must sample a longer trajectory when turning on the charges? > > > > > > I'm following the procedures of > > > http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial > > > > > > Does anyone know the reason for the discrepancy between these two > > > (seemingly identical) processes? > > > > > > Thanks, > > > Bob > > > > > > _______________________________________________ > > > 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 > > > > > > . > > > > > > > > > > _______________________________________________ > > 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 > > > _______________________________________________ > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
