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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