Thank you.<br>I read it and I understood your mean.<br><br><div class="gmail_quote">On Wed, Apr 6, 2011 at 11:52 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 class="im"><span>On 06/04/11, <b>mohsen ramezanpour </b> <<a href="mailto:ramezanpour.mohsen@gmail.com" target="_blank">ramezanpour.mohsen@gmail.com</a>> wrote:</span><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div>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></div>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>
<font color="#888888"><br>Mark</font><div><div></div><div class="h5"><br><br><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div><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" target="_blank">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>
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><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="_blank">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="_blank">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="_blank">Mark.Abraham@anu.edu.au</a><br>
> To: <a href="mailto:gmx-users@gromacs.org" target="_blank">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="_blank">vt.edu</a> |
(540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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