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? 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 >> > >
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