<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
mohsen ramezanpour skrev 2011-04-06 09.31:
<blockquote
cite="mid:BANLkTikA_tDbejmPsM8V0Soj+Up2ZjS_Og@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On Wed, Apr 6, 2011 at 11:53 AM, Erik
Marklund <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</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"> Hi,<br>
<br>
No we don't. You can't have fractions of elementary
particles in your molecules.<br>
<br>
</div>
</blockquote>
<div>Dear Erik<br>
<br>
Yes,You are right.It is obvious .<br>
But I wanted to simulate a part of my system.for example a
part of my protein!<br>
I was wrong,we can't do that <br>
<br>
</div>
</div>
</blockquote>
I think there are several examples of that in literature, e.g. by
Åqvist and coworkers. But think they use a different approach than
just cutting away part of the protein.<br>
<br>
Erik<br>
<blockquote
cite="mid:BANLkTikA_tDbejmPsM8V0Soj+Up2ZjS_Og@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<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"> Erik<br>
<br>
mohsen ramezanpour skrev 2011-04-06 09.13:
<div>
<div class="h5">
<blockquote 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"
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 text="#000000" bgcolor="#ffffff">
<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>
<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>
> gmx-users mailing
list <a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
> <a
moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the
archive at <a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
> Please don't post
(un)subscribe requests to
the list. Use the<br>
> www interface or
send it to <a
moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
</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>
========================================
<div>
<div><br>
-- <br>
gmx-users mailing list <a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive
at <a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post
(un)subscribe requests to
the list. Use the www
interface or send it to <a
moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</blockquote>
<br>
</div>
</div>
</div>
<br>
--<br>
gmx-users mailing list <a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a
moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the
list. Use the<br>
www interface or send it to <a
moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
</div>
<br>
</blockquote>
<br>
<br>
</div>
</div>
<pre 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 moz-do-not-send="true" href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a moz-do-not-send="true" href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a>
</pre>
</div>
<br>
--<br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
</div>
<br>
</blockquote>
<br>
<br>
<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>
</pre>
</body>
</html>