AMBER Archive (2003)

Subject: Re: AMBER: MD simulations on small molecules immersed in sparse water shell

From: rluo_at_uci.edu
Date: Tue Sep 16 2003 - 14:07:03 CDT

I don't know what PHS stands for. Do you mean the spherical boundary
potential?

In my PBMD simulations with shell waters. The restraining forces are
turned on when the waters are 9 A away from the surface of the protein.
This implementation is the same as the cap water setting except that the
boundary surface is not a sphere (set to be 9 A away from the surface
protein atoms).

Since we have Langevin Dynamics now, stochastic forces are also applied
to the waters to mimic the bulk. I believe this is the so-called
generalized stochastic potential for arbitrary boundary though with
long-range/reaction-field electrostatic correction taken care of by FDPB.

Best,
Ray

Carlos Simmerling wrote:
> is this meant to be like Roux's PHS water model,
> or does it work differently?
> Carlos
>
> ----- Original Message -----
> From: <rluo_at_uci.edu>
> To: <amber_at_scripps.edu>
> Sent: Tuesday, September 16, 2003 2:16 PM
> Subject: Re: AMBER: MD simulations on small molecules immersed in sparse
> water shell
>
>
>
>>I have a modified sander that applies the the cap restraining forces to
>>water molecules in such a setting.
>>
>>Best,
>>Ray
>>
>>Junmei Wang wrote:
>>
>>>
>>>
>>>
>>>Dear AMBER users:
>>>
>>>I am running non-periodic boundary MD simulations for a set of
>
> middle-sized
>
>>>molecules (50-100 atoms). Each is immersed in a sparse water shell (10
>
> to
>
>>>20 TIP3P water, generated using solvateshell in LEAP). What is the best
>
> way
>
>>>to keep solvent molecules from drifting away from the solute along the
>
> MD
>
>>>simulations? This is no water cap information in the topology files if
>>>solvent molecules are added using solvateshell instead of solvatecap.
>>>
>>>Thanks
>>>
>>>Junmei
>>>
>>>
>>>
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>>>.
>>>
>>
>>--
>>====================================================
>>Ray Luo, Ph.D.
>>Department of Molecular Biology and Biochemistry
>>University of California, Irvine, CA 92697-3900
>>Office: (949)824-9528 Lab: (949)824-9562
>>Fax: (949)824-8551 e-mail: rluo_at_uci.edu
>>Home page: http://rayl0.bio.uci.edu/rayl/
>>====================================================
>>
>>
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>
>
>
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-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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