<span>On 06/04/11, <b class="name">mohsen ramezanpour </b> <ramezanpour.mohsen@gmail.com> wrote:</span><blockquote cite="mid:BANLkTimHUHT40im=F7MokcEBdvBFUZk7bw@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Daer Dr.Mark<br /><br />You are right,But all of them(as I know) have integer charges!<br />the problem is simullating a system with partial charges.<br />We absolutely have such systems.</div></blockquote><br />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.<br /><br />Mark<br /><br /><blockquote cite="mid:BANLkTimHUHT40im=F7MokcEBdvBFUZk7bw@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div class="gmail_quote">On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br />
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000"><div class="im">
On 6/04/2011 4:45 PM, mohsen ramezanpour wrote:
<blockquote type="cite">Dear Dr.Justin<br />
<br />
What can we do (how can neutralize system) if the total charge of
our system was not integer?<br />
I think there is not any solution and we have to simulate a
charged system not a neutral.<br />
Am I right?<br />
</blockquote>
<br /></div>
I suspect every tutorial for simulating proteins in water deals with
the need for counter-ions, and the technique for generating them.<br /><font color="#888888">
<br />
Mark</font><div><div ><br/></div><div class="h5"><br />
<br />
<blockquote type="cite">
Thanks in advance<br />
<br />
<div class="gmail_quote">On Wed, Apr 6, 2011 at 11:12 AM, mohsen
ramezanpour <span dir="ltr"><<a href="mailto:ramezanpour.mohsen@gmail.com" target="1">ramezanpour.mohsen@gmail.com</a>></span>
wrote:<br />
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear Dr.Justin<br />
<br />
I had the same problem.<br />
I modified the charges and charge groupsin the topology of a
drug.the net charge of it is zero(I am sure)<br />
though,when I used pdb2gmx it resulted a NOTE like the
following:<br />
<br />
NOTE:The system has non-zero total charge: 3.000003e00<br />
I continued simulation and ignored it!<br />
Because:<br />
1- I checked my protein.top and qtot was 3<br />
2-the net charge of my drug was 0<br />
3-Besides,all charges have 3 digit precision,How can it have
0.000003 additional charge?!<br />
<br />
What is your point of view?<br />
Thanks in advance for your reply
<div>
<div><br />
<br />
<br />
<div class="gmail_quote">On Wed, Apr 6, 2011 at 3:40 AM,
Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="1">jalemkul@vt.edu</a>></span>
wrote:<br />
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><br />
<br />
김현식 wrote:<br />
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br />
<br />
> Date: Tue, 5 Apr 2011 23:43:19 +1000<br />
> From: <a href="mailto:Mark.Abraham@anu.edu.au" target="1">Mark.Abraham@anu.edu.au</a><br />
> To: <a href="mailto:gmx-users@gromacs.org" target="1">gmx-users@gromacs.org</a><br />
> Subject: Re: [gmx-users] How to remove
charge of 5e-2 ??<br />
><br />
> On 5/04/2011 11:17 PM, Hyunsik wrote:<br />
> > Dear experts,<br />
> ><br />
> > Hi,<br />
> ><br />
> > When prepare a system, the system had
+5.5. So I add 5 CL- ion to neutralize.<br />
> ><br />
> > But as you know, the Cl charge is -1
and there still is 5e-2. how can i remove that.<br />
><br />
> Your statements are inconsistent. If you had
5.5 charge and added five<br />
> chloride ions, you could not end up with
0.05.<br />
<br />
oh.. I have mistaken.. I had 5.005 of the system
charge.<br />
So even if added five choride ions, the system
charge is not zero. there was 0.005<br />
<br />
that is partial charge?? If like that, topology
is broken or something wrong? abnormal??<br />
<br />
</blockquote>
<br />
</div>
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.<br />
<br />
-Justin
<div><br />
<br />
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Thank you,<br />
<br />
Hyun<br />
<br />
><br />
> Mark<br />
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-- <br />
========================================<br />
<br />
Justin A. Lemkul<br />
Ph.D. Candidate<br />
ICTAS Doctoral Scholar<br />
MILES-IGERT Trainee<br />
Department of Biochemistry<br />
Virginia Tech<br />
Blacksburg, VA<br />
jalemkul[at]<a href="http://vt.edu" target="1">vt.edu</a> |
(540) 231-9080<br />
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="1">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br />
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