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Hi,<br>
<br>
No we don't. You can't have fractions of elementary particles in
your molecules.<br>
<br>
Erik<br>
<br>
mohsen ramezanpour skrev 2011-04-06 09.13:
<blockquote
cite="mid:BANLkTimHUHT40im=F7MokcEBdvBFUZk7bw@mail.gmail.com"
type="cite">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.<br>
<br>
<div class="gmail_quote">On Wed, Apr 6, 2011 at 11:22 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
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 text="#000000" bgcolor="#ffffff">
<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 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
moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
> To: <a moz-do-not-send="true"
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>
> --<br>
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</blockquote>
<br>
</div>
-- <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 moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a>
| (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================
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<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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