Great discussion! While (seemingly) small changes in cut-off can give considerable performance improvements and therefore it is worth considering such tweaks in simulation settings, these finding highlight the importance of not changing settings blindly.
Cheers, -- Szilárd On Wed, Jan 30, 2013 at 2:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/29/13 11:57 PM, James Starlight wrote: > >> Justin, >> >> >> with cut-offs=1.2 both in cpu+gpu or with cpu only I've obtained only >> small decrease along the Z-dim ( from 10 to 9 nm). With cut-offs 1.0 >> I've obtained decreae from 10 to 8.5. So it might be concluded that >> the observable is cut-off sensetive. >> >> > Good to know. Most "normal" systems of proteins in water will probably be > insensitive to most changes with the new cutoff scheme, but I was > suspicious about membranes. I'll have to do some of my own testing, as > well. > > > By the way during simulation of such system in gromos-54a7 united atom >> ( the same number of lipids and water) ff with 1.2 cut-offs I didnt >> observed any decrease of the cutoffs. >> >> > Different force fields behave differently. I wouldn't expect to > necessarily be able to draw a parallel between different parameter sets > that inherently use different run parameters, but this is also good to know. > > -Justin > > > 2013/1/29 Justin Lemkul <jalem...@vt.edu>: >> >>> >>> >>> On 1/29/13 2:19 AM, James Starlight wrote: >>> >>>> >>>> One important point: >>>> >>>> in that simulations I've used decreased cut-offs with charmm36 ff >>>> because that systems have been modelled with CPU+GPU so I had some >>>> imbalance in cpu\gpu loadings with common (1.2) cutoffs. >>>> >>>> rlist = 0.8 ; Cut-off for making neighbor list >>>> (short >>>> range forces) >>>> rlistlong = 1.4 >>>> rcoulomb = 0.8 ; long range electrostatic cut-off >>>> rvdw = 0.8 >>>> >>>> >>>> Might that affect on the compresbility of my system? Might I prevent >>>> such compression by means of changing ref_p or compressibility on the >>>> Z using emiisotropic pcoupltype? >>>> >>>> >>> Membranes are very sensitive to cutoff settings. Can you test by >>> running on >>> CPU only with the normal CHARMM cutoff settings? I would be curious to >>> see >>> if the shortened cutoffs produce bad results. >>> >>> You should not have to make any special changes to the compressibility or >>> pressure along Z in order for the simulation to be stable. What's >>> happening >>> to the x and y box vectors? Is the membrane becoming distorted or >>> compressed? Or is it expanding laterally? >>> >>> >>> >>> 2013/1/29 James Starlight <jmsstarli...@gmail.com>: >>>> >>>>> >>>>> Its intresting that on the same system which was equilibrated longer >>>>> the decrease on the Z dim was smaller (from 10 to 9nm). By the way >>>>> does it possible to simulate membrane proteins (with explicit >>>>> membrane) in the nvt enssemble without explicit barostat ? What >>>>> options in the mdp should be added for such simulation ? >>>>> >>>>> >>> Certainly you can run in an NVT ensemble if the force field will produce >>> good results. Normally NPT or NPAT ensembles are most appropriate for >>> membranes, depending on the parameterization of the lipids. Running in >>> NVT >>> is as simple as setting "pcoupl = no" while leaving other >>> thermostat-related >>> items the same. >>> >>> -Justin >>> >>> >>> >>>>> James >>>>> >>>>> 2013/1/28 Justin Lemkul <jalem...@vt.edu>: >>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 1/28/13 8:45 AM, James Starlight wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> Justin, >>>>>>> >>>>>>> yes, 2 A for C atoms. >>>>>>> >>>>>>> The dims are 8.68740 8.41864 10.00000 >>>>>>> >>>>>>> >>>>>> Well, with such a dramatic change, it should be fairly easy to simply >>>>>> watch >>>>>> the trajectory and see what went wrong. >>>>>> >>>>>> >>>>>> -Justin >>>>>> >>>>>> -- >>>>>> ==============================**========== >>>>>> >>>>>> Justin A. Lemkul, Ph.D. >>>>>> Research Scientist >>>>>> Department of Biochemistry >>>>>> Virginia Tech >>>>>> Blacksburg, VA >>>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>>>>> >>>>>> ==============================**========== >>>>>> -- >>>>>> gmx-users mailing list gmx-users@gromacs.org >>>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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 gmx-users-requ...@gromacs.org. >>>>>> * Can't post? Read >>>>>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>>>> >>>>> >>> >>> -- >>> ==============================**========== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> >>> ==============================**========== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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 gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 gmx-users-requ...@gromacs.org. > * Can't post? 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