Hi,
I guess no one has responded because there isn't a definitive answer
to your question. Conventional wisdom is that the choice of cutoff for
a solvated system using PME is somewhat arbitrary beyond 8 Ang.
(although I am sure there are people who will disagree with this).
Direct space cutoff matters much more for more condensed phase
systems, like membranes. If your ultimate goal is to make sure your
proteins are not interacting by the end of the simulation, you
probably need to run separate simulations of each protein "part" so
that you have a baseline of how the non-interacting systems behave
(although getting converged data could be challenging if your systems
are large). Then you can compare your two part system to the two
independent systems. However, if all you are interested is the
separation event, maybe it is not so important that you have
completely non-interacting systems.
One analysis you may find useful is the 'minimage' command in cpptraj,
which will calculate the minimum non-self imaged distance between
atoms in two masks so you can track the closest approach of each part
to each other.
Hope this helps,
-Dan
On Wed, Jul 5, 2017 at 1:26 PM, Dmitry Suplatov <genesup.gmail.com> wrote:
> Dear Amber users,
>
> since no one replied I shall rephrase my question.
>
> My protein has two parts, covalently connected, which move 40A away from
> each other during the MD. The cell dimensions were set to at least 30A
> from the protein to the cell edge. Therefore, one part of my protein has
> extended into the neighbouring cell. My cutoff (cut) was set to 10.
> Would it be correct to assume that my results are accurate enough
> because the initial distance between the protein molecules in
> neighbouring cells is at least 30 x 2 = 60A, and after the protein has
> moved there would still be at least 60A - 40A = 20A gap between the two
> protein copies, which is more than 10A cutoff?
>
> Thank you for your time.
>
> P.S. Actually, I am interested only in the initial event - the two parts
> of the protein separate, i.e., they do not form a stable globule. I do
> not care what exactly happens afterwards.
>
>
> On 07/03/2017 09:32 PM, Dmitry Suplatov wrote:
>> Dear Amber users,
>>
>> I need to simulate a two-domain protein. The two domains are expected
>> to separate during the MD. How should I select the solvation distance
>> when creating a box? I.e., the box should accommodate a two-domain
>> protein which becomes longer when the domains separate during the MD.
>>
>> My understanding is that the protein in the cell #1 must not approach
>> the protein in the cell #2 closer than the specified by the 'cut'
>> parameter (the close range electrostatics). Therefore, if, e.g., I
>> have used the 'at least 25A' solvation distance and after the
>> simulation I put the two cells together in PyMol and the two proteins
>> are at least 'cut' A away from each other - than its OK. Am I right?
>>
>> Thanks.
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Jul 10 2017 - 06:30:06 PDT
