Re: Is it necessary to neutralize the system with NAMD program?

From: Aaron Oakley (oakley_at_rsc.anu.edu.au)
Date: Tue Mar 16 2004 - 16:18:00 CST

My experience mirrors Brian's.
I've done several simulations > 1ns,
using PME with and without counterions
with no overall differences.

However, I think it would be important
to include counterions where DNA/RNA
are involved, because of the concentration of
charge near the nucleotide backbone.
Can anyone comment on this?

Cheers,

Aaron

On 17/03/2004, at 6:07 AM, Brian Bennion wrote:

>
> I read the same email message on ccl.
>
> I have thought about this problem as well and have tested systems both
> ways.
>
> I was taught that ions, unless specifically needed in the protein
> structure, were superflous. The water screens the charge on any ion
> within 4-6 angstroms. However, these simulations were not using PME.
>
> My results with and without counterions are equivalent. (ie temp,
> pres,
> gpress values are within 1-2% at 0.25ns and 11.0ns for a system with
> 65K
> atoms and a net +3 charge.
>
>
> If any one else has a contrary info I would love to here it.
>
> If you choose to add counter ions, the vmd plugin autoionize might be
> what
> you need.
>
> Regards
> Brian
>
> PS
> Contrary to what the ccl list member said. We are not even close to
> real-life conditions even without PBC. Thats what ab-initio MD is for!!
>
>
>
>
> On Sun, 14 Mar 2004 yxiong_at_mail.ccnu.edu.cn wrote:
>
>> Dear sir,
>> I have doing MD at a charged system with PME method and Periodic
>> Boundary
>> Conditions.
>> I see the information as following in CCL mailing list:
>> --------------------------------------------------------------
>> When you use periodic boundary conditions, you are effectively
>> simulating an infinite system. With a non-zero total charge, you then
>> get an infinite total charge and an infinite potential energy. Such a
>> system would not be stable under real-life conditions (i.e. without
>> the
>> artifact of periodic boundary conditions). In fact, if you simulate
>> such a system at constant pressure, i.e. with a variable box size, you
>> will see the volume go up systematically.
>> -----------------------------------------------------------------
>> I want to get the geometry of system. Is it necessary to neutralize
>> the
>> system with NAMD program? If yes, how can I neutralize the system
>> easily?
>>
>> Thank you for your advice!
>>
>>
>>
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
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