On Tue, Jul 26, 2016 at 7:54 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 7/26/16 1:16 PM, Alexander Alexander wrote: > >> On Tue, Jul 26, 2016 at 6:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 7/26/16 11:27 AM, Alexander Alexander wrote: >>> >>> Thanks. >>>> >>>> Yes indeed it is a free energy calculation in which no problem showed up >>>> in >>>> the first 6 windows where the harmonic restrains were applying on my >>>> amino >>>> acid but the DD problem came up immediately in the first windows of the >>>> removing charge. Below please find the mdp file. >>>> And If I use -ntmpi = 1 then it takes ages to finish. Although my >>>> gromcas >>>> need to be compiled again with thread-MPI . >>>> >>>> >>>> I suspect you have inconsistent usage of couple-intramol. Your >>> long-distance LJC pairs should be a result of "couple-intramol = no" in >>> which you get explicit intramolecular exclusions and pair interactions >>> that >>> occur at longer distance than normal 1-4 interactions. If you ran other >>> systems without getting any problem, you probably had "couple-intramol = >>> yes" in which all nonbonded interactions are treated the same way and the >>> bonded topology is the same. >>> >>> >> Actually I always have had "couple-intramol = no" in all my other >> calculation(a single amino acid in water solution), and not problem has >> shown up. But FEP calculations of the charged amino acid where I have also >> an Ion for neutralization of the system and "ion+amino acid" is used as >> "couple-moltype", this problem emerges. And if you noticed the Ion here CL >> is always one of the atom involving in the problem. I hope >> "couple-intramol >> = yes"can sove the problem in charged amino acid. >> >> > Well, there are implications for the results. Consider what it says in > the manual. But yes, this is your problem. You've got physically separate > molecules that you call one [moleculetype] for the purpose of > transformation, and you're running into a problem that isn't really > physically meaningful in any way. > Actually yes, Ion and amino acid both as [moleculetype]are really far away from each other. But I usually use the final .gro file of the last step as input file in the new step, and this separation is what that gro file has. I hope " couple-intramol = yes" can help. > > >>> Another question is that if really this amount of pull restrain is >>> >>>> necessary to be applied on my molecules (singke amino acid) before >>>> removing >>>> the charge and vdW? >>>> >>>> >>>> You're decoupling a single amino acid? What purpose do the pull >>> restraints even serve? CA-HA, etc. should be bonded in a single amino >>> acid, so why are you applying a pull restraint to them? I really don't >>> understand. >>> >>> >> I want to make sure sudden conformational changes of amino acid do not >> occur during the perturbation. In particular, when the charge is turned >> off. Applying a harmonic restraint to keep the geometry the same during >> FEP is a well-established procedure, e.g. Deng, Y.; Roux, B. J Chem Theory >> Comput 2006, 2 (5), 1255. I might reduce the number of restraints to only >> between 1 or 2 pairs. >> >> > Preserving the A-state in the bonded topology (and using couple-intramol = > no) will prevent any weirdness from happening without needing any of these > restraints. As in my previous message, restraining CA-HA with a harmonic > potential makes no sense at all. Those atoms have a bond between them. > The pull code is not doing anything useful. > Then, If the " couple-intramol = yes" hopefully solves the problem discussed above, then, maybe applying restrain in the presence of " couple-intramol = yes" is not avoidable. > > The whole task is to calculate the binding free energy of amino acid to a >> metal surface, although here I am still dealing with the amino acid in >> only >> water without surface yet. >> > > I believe I've mentioned this before, but in case it got lost along the > way - using the free energy decoupling technique is a very ineffective way > of calculating this binding free energy. Do a PMF. It's extremely > straightforward and you don't deal with any of these algorithmic problems. > It will also likely converge a lot faster than try to do complex decoupling. > Actually I should have known this in beginning, but, now is a bit late for me to switch to PMF. Best regard, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.