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: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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(http://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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