David, > > Correct, but I made some changes to ensure correct storing of > values in the > > tpr file. Correct me if I am wrong, but the storage of these values > only > > occurs during the generation of a tpr file with grompp. > > Are you sure this worked properly? I tried to do this myself at one > point and couldn't find the bug that was causing the problem. > > To check it, you should gmxdump your tpr file and look for the cpA, > cpB, etc parameters for the angle restraint in question. Every time I > did it, one of these was zero. > I did this already and with gmxdump it returned all four parameters (cpA, cpB, PhiA, PhiB) as input. But what I do not know is if these parameters can be changed afterwards (perhaps in mdrun). I do not expect this, but I am not sure it will not happen.
> Also, if you are using 3.3.1, you would need to modify the angle > restraints code to *use* these parameters again, since as I mentioned > before, the "fix" in 3.3.1 was to make angle restraints always use > the > A state parameters. I removed this fix, before implementing my own. If you are interested you can find it on bugzilla or I can send it to you. > > > I am not sure if there are other bugs in the angle restraints > value. If so > > this might explain why the dG/dl crosses zero. I do not understand > it > > otherwise. > > I don't think there are any other bugs; I've used this code a lot > now. > But it's possible. You could try computing something where you know > what the answer should be. > > It could cross zero if your angle restraints were turning off, I > think. I do not understand this. Turning the restraints off is only affecting the highed of dG/dl and turning it off means that you slowly go to zero. Maarten Send instant messages to your online friends http://uk.messenger.yahoo.com _______________________________________________ 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