Thank you. I read it and I understood your mean. On Wed, Apr 6, 2011 at 11:52 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> On 06/04/11, *mohsen ramezanpour * <ramezanpour.moh...@gmail.com> wrote: > > 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. > > > Read the other link I provided. 3.000003e00 indicates integer charge. One > neutralizes it with a set of ions that have a net charge of -3. > > Mark > > > 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: >>> >>>> >>>> >>>> κΉνμ 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 >> > > > -- > 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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