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 <mailto: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
<mailto:jalem...@vt.edu>> wrote:
김현식 wrote:
> Date: Tue, 5 Apr 2011 23:43:19 +1000
> From: mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
> To: gmx-users@gromacs.org <mailto: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
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--
========================================
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
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