AMBER Archive (2009)

Subject: [AMBER] TMD: solvation and equilibration questions

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Fri Jul 10 2009 - 20:07:55 CDT

Dear AMBER users,
 
Sorry that I used a wrong title in my last post. Please skip my last message. Thanks  Carlos for reminding  me.
 
My questions are:

   We are going to study the conformational change of protein between two different states by using TMD methods. I have some confusions about TMD and request your help.

I list my questions as follows:

Suppose we have two conformations for a protein system, titled "A" and "B". I am going to check the conformational change from A to B.

1. Should the initial structure (A state) be equilibrated before starting the TMD simulation? If so, the starting conformation (A' state) in TMD is not the same as the initial conformation (A state). Then does this simulation represent one of the possible the pathways from A to B?

2. How should I solvate the protein, in implicit or explicit waters? I noticed that someone uses the water shell, not a box full of water, to solvate the solute. What the difference between the two choices? Which one should I use?

3. We used the full explicit solvation of protein in the conventional MD for 15 ns. Can I start the TMD simulation from an equilibrated snapshot, e.g. the snapshot at 3 ns?

Thanks so much.
   
Jeffrey

-----------------------------------------------
 
  State Key Lab. of Molecular Reaction  Dynamics(SKLMRD),
  Dalian Institute of Chemical Physics(DICP),
  the Chinese Academy of Sciences(CAS),
 
  Zhongshan Road457, Dalian City,
  Liaoning Province 116023,P. R.  China

--- 09年7月11日，周六, Carlos Simmerling <carlos.simmerling_at_gmail.com> 写道：

发件人: Carlos Simmerling <carlos.simmerling_at_gmail.com>
主题: TMD: was: Re: [AMBER] charges in topology file
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年7月11日,周六,上午12:36

I suggest always making sure the subject matches your question, because a
subject about charges might make someone who could help with TMD skip the
email.

2009/7/10 Jeffrey <jeffry20072008_at_yahoo.cn>

> Dear AMBER users,
>
>   We are going to study the conformational change of protein between two
> different states by using TMD methods. I have some confusions about TMD and
> request your help.
>
> I list my questions as follows:
>
> Suppose we have two conformations for a protein system, titled "A" and "B".
> I am going to check the conformational change from A to B.
>
> 1. Should the initial structure (A state) be equilibrated before starting
> the TMD simulation? If so, the starting conformation (A' state) in TMD is
> not the same as the initial conformation (A state). Then does this
> simulation represent one of the possible the pathways from A to B?
>
> 2. How should I solvate the protein, in implicit or explicit waters? I
> noticed that someone uses the water shell, not a box full of water, to
> solvate the solute. What the difference between the two choices? Which one
> should I use?
>
> 3. We used the full explicit solvation of protein in the conventional MD
> for 15 ns. Can I start the TMD simulation from an equilibrated snapshot,
> e.g. the snapshot at 3 ns?
>
> Thanks so much.
>
> Jeffrey
>
>
>
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