Well, gromacs is not the only software available. I'd still ask them and then try it in gromacs after parsing. \If there is a difference, then try in NAMD and/or charmm. I know that this is the gromacs users list, but we're talking about debugging here and I think that getting the original parameter file and interpreting to gromacs or exactly rerunning in charmm is still the best way to go.
If he can reproduce it in charmm, but not in gromacs, then the problem becomes more well defined. I stand by my advice. Chris. -- original message -- Peter C. Lai pcl at uab.edu Wed Aug 15 21:09:31 CEST 2012 Previous message: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? Next message: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] On 2012-08-15 06:55:59PM +0000, Christopher Neale wrote: > Write the authors of the simulation paper that has a "correct" APL for POPE > and ask them for an input file. > That is really the only way to be sure that you are not doing something > different than they did. > In my experience, people are quite willing to provide you with their input > file(s). > If you still get a different APL than they reported, then see if your > simulation times are similar and repeat your run > a few times to see if it's just statistical noise. The fundamental problem Sebastian will have is that Klauda obtained their APLs using CHARMM software, and he is trying to reproduce this using the forcefield in Gromacs software. So even if the CHARMM input files were provided, it maybe difficult to exactly reproduce the conditions in Gromacs (if certain parameters were implemented differently) > > Regarding 323 K, I don't recall... it's just a number that sticks in my head. > Perhaps it is for DPPE or DPPC. > > I'd still suggest that you at least try POPC. So your peptide binds more > favourably to POPE than to POPC... > that alone does not limit you to POPE. Then again, I don;t know exactly what > you are trying to do. > > Chris. > It is generally a good idea to use a higher temp than the phase transition temperature, since during equilibration close to the phase transition temp there is a risk of inducing some ordering due to uneven heating. People run DPPC at 323 because its phase transition temp is 315K. If POPC's is 271 and people typically run POPC at 300, then it may be wise to bump up the running temp of a POPE system. Of course, your APL will inflate at higher temperatures... > > -- original message -- > > > My peptide is known to be more favorably to PE than PC membrane that is why I > am using POPE. > > Experimentally, the liquid phase transition is at 298K for POPE (if I am not > mistaken). Is your 323K refer to some simulations? > > At first I wanted to use the new CHARMM36 lipids parameters because they are > supposed to solve the previous CHARMM27 issue with the area per lipid. > However, I am consistently obtained smaller APL then experiment and I am not > able to reproduce the published APL obtained for POPE, even if I am starting > from their equilibrated 80-POPE membrane and use same simulation conditions. > That was the reason for starting this thread on the mailing list. > > Unfortunately, my peptide conformational space in solution is only > well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use > Berger's lipid parameters with OPLS or GROMOS even if it would be preferable > as they do not have APL inconsistency and are united-atom. > > I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be > made neglegible by using bigger membrane compared to my peptide's size (?). > > Sebastien -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
