Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be taken into account at infinite cutoff or omitted?
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> >>>>>>>> <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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