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. -JustinOn 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 vdwparameters...So I need pbc as well. Sorry, this doesn't make much sense to me. If you're using implicitsolvent (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.comwrote: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 doingnothing 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>beforeposting!* 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><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>beforeposting! * 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. 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>-- ==============================**==================== 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 <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? Read 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
