mohsen ramezanpour skrev 2011-04-06 09.31:
On Wed, Apr 6, 2011 at 11:53 AM, Erik Marklund <er...@xray.bmc.uu.se
<mailto:er...@xray.bmc.uu.se>> wrote:
Hi,
No we don't. You can't have fractions of elementary particles in
your molecules.
Dear Erik
Yes,You are right.It is obvious .
But I wanted to simulate a part of my system.for example a part of my
protein!
I was wrong,we can't do that
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.
Erik
Erik
mohsen ramezanpour skrev 2011-04-06 09.13:
Daer Dr.Mark
You are right,But all of them(as I know) have integer charges!
the problem is simullating a system with partial charges.
We absolutely have such systems.
On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:
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:
??? 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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MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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