I am not using any solvent. I mimic the presence of water by vdw tabulated potentials. I wish to see what electrostatics will change. And the coulomb cutoff = 0 will completely remove the electrostatic, right?
On Wed, Sep 4, 2013 at 3:23 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/4/13 10:20 AM, Steven Neumann wrote: > >> Sorry it is a vacuum but I included implicit solvent in vdw >> parameters...So >> I need pbc as well. >> >> >> > Sorry, this doesn't make much sense to me. If you're using implicit > solvent (GB), then it's by definition not vacuum. I also find the same to > be true - finite cutoffs lead to artifacts in vacuo or when using GB. The > only stable simulations I have produced using GB us the all-vs-all settings > I showed below. Obviously, if your parameterization and tabulated > interactions have different requirements, then what I said goes out the > window, but using GB with PBC also suffers from artifacts. > > -Justin > > On Wed, Sep 4, 2013 at 3:18 PM, Steven Neumann <s.neuman...@gmail.com >> >wrote: >> >> Thank you. i am using my own vdw tables so need a cut off. >>> >>> >>> >>> >>> On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 9/4/13 10:11 AM, Steven Neumann wrote: >>>> >>>> Thank you! Would you suggest just a cut-off for coulmb? >>>>> >>>>> >>>>> Not a finite one. The best in vacuo settings are: >>>> >>>> pbc = no >>>> rlist = 0 >>>> rvdw = 0 >>>> rcoulomb = 0 >>>> nstlist = 0 >>>> vdwtype = cutoff >>>> coulombtype = cutoff >>>> >>>> -Justin >>>> >>>> On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul <jalem...@vt.edu> >>>> wrote: >>>> >>>>> >>>>> >>>>> >>>>>> On 9/4/13 10:03 AM, Steven Neumann wrote: >>>>>> >>>>>> DEa Users, >>>>>> >>>>>>> >>>>>>> My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. >>>>>>> I >>>>>>> want >>>>>>> to use PME in my mdp: >>>>>>> >>>>>>> rcoulomb = 2.0 >>>>>>> coulombtype = PME >>>>>>> pme_order = 4 >>>>>>> fourierspacing = 0.12 >>>>>>> >>>>>>> The cutoff needs to stay like this, I have my own tables with VDW, >>>>>>> bonds, >>>>>>> angles and dihedrals. >>>>>>> >>>>>>> i got the NOTE: >>>>>>> >>>>>>> The optimal PME mesh load for parallel simulations is below 0.5 >>>>>>> and for highly parallel simulations between 0.25 and 0.33, >>>>>>> for higher performance, increase the cut-off and the PME grid >>>>>>> spacing >>>>>>> >>>>>>> what setting would you suggest to use on 8 CPUs? >>>>>>> >>>>>>> >>>>>>> I would suggest not using PME :) The problem is PME is extremely >>>>>>> >>>>>> inefficient in vacuo because it spends a lot of time doing nothing due >>>>>> to >>>>>> the empty space. Moreover, you're not likely really simulating in >>>>>> vacuo >>>>>> at >>>>>> that point because you've got PBC and therefore are really doing a >>>>>> simulation in more of a diffuse crystal environment, so there are >>>>>> probably >>>>>> artifacts. >>>>>> >>>>>> -Justin >>>>>> >>>>>> -- >>>>>> ==============================******==================== >>>>>> >>>>>> >>>>>> >>>>>> Justin A. Lemkul, Ph.D. >>>>>> Postdoctoral Fellow >>>>>> >>>>>> Department of Pharmaceutical Sciences >>>>>> School of Pharmacy >>>>>> Health Sciences Facility II, Room 601 >>>>>> University of Maryland, Baltimore >>>>>> 20 Penn St. >>>>>> Baltimore, MD 21201 >>>>>> >>>>>> jalemkul@outerbanks.umaryland.******edu <jalemkul@outerbanks.** >>>>>> umaryland.edu >>>>>> <jalemkul@outerbanks.**umaryland.edu<jalem...@outerbanks.umaryland.edu>>> >>>>>> | (410) >>>>>> 706-7441 >>>>>> >>>>>> ==============================******==================== >>>>>> >>>>>> -- >>>>>> gmx-users mailing list gmx-users@gromacs.org >>>>>> http://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users> >>>>>> <htt**p://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>>> > >>>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users> >>>>>> <h**ttp://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<**h**ttp://www.gromacs.org/**Support/**<http://www.gromacs.org/Support/**> >>>>>> >>>>>> Mailing_Lists/Search<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> >>>>>> <http://**www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>>>>> > >>>>>> <http://**www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/Support/**Mailing_Lists> >>>>>> <http:/**/www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>>>> > >>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>> ==============================****==================== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Postdoctoral Fellow >>>> >>>> Department of Pharmaceutical Sciences >>>> School of Pharmacy >>>> Health Sciences Facility II, Room 601 >>>> University of Maryland, Baltimore >>>> 20 Penn St. >>>> Baltimore, MD 21201 >>>> >>>> jalemkul@outerbanks.umaryland.****edu <jalemkul@outerbanks.** >>>> umaryland.edu <jalem...@outerbanks.umaryland.edu>>| (410) >>>> 706-7441 >>>> >>>> ==============================****==================== >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>> <htt**p://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<h**ttp://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. 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Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > 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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