Carla Jamous skrev:
Thank you Justin,
but I ran a simulation before this one with GTP & it worked fine. GDP
& GTP parameters are identical except for GDP having less atoms.
This is why I can't understand why I don't get an integer charge while
I did in my previous simulation.
Carla
Well, if you removed one phosphate group you may not have removed
exactly -1 e. What do the rtp-entries look like?
Erik
On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Carla Jamous wrote:
Hi,
In order to run my simulation, I had to insert GDP parameters
in ffamber94 (the force field I'm using).
However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an
integer. But I'm getting a decimal charge which gives me
naturally a decimal total charge of my molecule.
I checked number of atoms, it's correct, their charge also.
But it seems it's having trouble adding charges & giving an
integer charge.
Does anyone have an idea where is the source of the problem?
What is the charge? If it is a small difference between an
integer and your charge (i.e., the difference between +1.9999 and
+2) then there is no problem. The issue there is the inherent
limitation of doing a lot of floating-point operations to sum the
total charge. If, however, you have a charge of +1.9256 when you
wanted +2, then your parameters are simply wrong.
-Justin
Thanks
Carla
--
========================================
Justin A. Lemkul
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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