Daer Dr.Mark You are right,But all of them(as I know) have integer charges! the problem is simullating a system with partial charges. We absolutely have such systems.
On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 6/04/2011 4:45 PM, mohsen ramezanpour wrote: > > Dear Dr.Justin > > What can we do (how can neutralize system) if the total charge of our > system was not integer? > I think there is not any solution and we have to simulate a charged system > not a neutral. > Am I right? > > > I suspect every tutorial for simulating proteins in water deals with the > need for counter-ions, and the technique for generating them. > > Mark > > > Thanks in advance > > On Wed, Apr 6, 2011 at 11:12 AM, mohsen ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > >> Dear Dr.Justin >> >> I had the same problem. >> I modified the charges and charge groupsin the topology of a drug.the net >> charge of it is zero(I am sure) >> though,when I used pdb2gmx it resulted a NOTE like the following: >> >> NOTE:The system has non-zero total charge: 3.000003e00 >> I continued simulation and ignored it! >> Because: >> 1- I checked my protein.top and qtot was 3 >> 2-the net charge of my drug was 0 >> 3-Besides,all charges have 3 digit precision,How can it have 0.000003 >> additional charge?! >> >> What is your point of view? >> Thanks in advance for your reply >> >> >> >> On Wed, Apr 6, 2011 at 3:40 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: >> >>> >>> >>> 김현식 wrote: >>> >>>> >>>> >>>> > Date: Tue, 5 Apr 2011 23:43:19 +1000 >>>> > From: mark.abra...@anu.edu.au >>>> > To: gmx-users@gromacs.org >>>> > Subject: Re: [gmx-users] How to remove charge of 5e-2 ?? >>>> > >>>> > On 5/04/2011 11:17 PM, Hyunsik wrote: >>>> > > Dear experts, >>>> > > >>>> > > Hi, >>>> > > >>>> > > When prepare a system, the system had +5.5. So I add 5 CL- ion to >>>> neutralize. >>>> > > >>>> > > But as you know, the Cl charge is -1 and there still is 5e-2. how >>>> can i remove that. >>>> > >>>> > Your statements are inconsistent. If you had 5.5 charge and added >>>> five >>>> > chloride ions, you could not end up with 0.05. >>>> >>>> oh.. I have mistaken.. I had 5.005 of the system charge. >>>> So even if added five choride ions, the system charge is not zero. >>>> there was 0.005 >>>> >>>> that is partial charge?? If like that, topology is broken or something >>>> wrong? abnormal?? >>>> >>>> >>> >>> Maybe, maybe not. Rounding errors could account for this difference, >>> especially if your system is very large. Still, you should inspect your >>> topology/topologies for inconsistencies. If pdb2gmx created the topology, >>> keep an eye on the "qtot" column for a running total of the charge. If >>> you've made or adjusted any topologies on your own, double-check your work. >>> If everything looks correct, then the difference is likely a consequence of >>> floating-point math and nothing more. >>> >>> -Justin >>> >>> >>> Thank you, >>>> >>>> Hyun >>>> >>>> > >>>> > Mark >>>> > -- >>>> > 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 >>>> >>>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> 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 >>> 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 >>> >> >> > > > -- > 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 >
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