Thanks a lot!
On Wed, Sep 4, 2013 at 3:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/4/13 10:44 AM, Steven Neumann wrote: > >> Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be >> taken into account at infinite cutoff or omitted? >> >> > As I said, setting the cutoffs to zero does not omit interactions. The > zero is used to trigger infinite cutoffs. > > -Justin > > >> On Wed, Sep 4, 2013 at 3:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 9/4/13 10:35 AM, Steven Neumann wrote: >>> >>> 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? >>>> >>>> >>>> No, it does the opposite. Setting all cutoffs to zero triggers the >>> all-vs-all kernels, which calculate every possible interaction. >>> >>> -Justin >>> >>> >>> 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.****umaryla**nd.edu<http://** >>>>>>>>>> umaryland.edu <http://umaryland.edu>> >>>>>>>>>> <jalemkul@outerbanks.**umaryla**nd.edu <http://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> >>>>>>>>>> <**http://lists.gromacs.org/********mailman/listinfo/gmx-users<http://lists.gromacs.org/******mailman/listinfo/gmx-users> >>>>>>>>>> > >>>>>>>>>> <ht**tp://lists.gromacs.org/********mailman/listinfo/gmx-users<http://lists.gromacs.org/******mailman/listinfo/gmx-users> >>>>>>>>>> **<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> >>>>>>>>>> **<http://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> >>>>>>>>>> <h**ttp://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> >>>>>>>>>>> **<http://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> >>>>>>>>>> <h**ttp://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> >>>>>>>>>> <h**ttp://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/*** >>>>>>>>>> *** <http://www.gromacs.org/****> >>>>>>>>>> Support/** >>>>>>>>>> <http://www.gromacs.org/****Support/**<http://www.gromacs.org/**Support/**> >>>>>>>>>> >< >>>>>>>>>> http://www.gromacs.**org/**Support/**<http://www.gromacs.** >>>>>>>>>> org/Support/** <http://www.gromacs.org/Support/**>> >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> Mailing_Lists/Search<http://******www.gromacs.org/Support/**<h** >>>>>>>>>> ttp://www.gromacs.org/Support/****<http://www.gromacs.org/Support/**> >>>>>>>>>> > >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Mailing_Lists/Search<http://****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. 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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 <jalemkul@outerbanks.** >>>>>>>> umaryland.edu >>>>>>>> <jalemkul@outerbanks.**umaryla**nd.edu<http://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> >>>>>>>> <ht**tp://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> >>>>>>>> > >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> <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> >>>>>>>> > >>>>>>>> <h**ttp://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/** <http://www.gromacs.org/**Support/**>< >>>>>>>> http://www.gromacs.**org/Support/**<http://www.gromacs.org/Support/**> >>>>>>>> > >>>>>>>> Mailing_Lists/Search<http://****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. 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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> >>>>>>>> > >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> <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 >>>>> <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. 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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 <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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