TMD: was: Re: [AMBER] charges in topology file

From: Carlos Simmerling <>
Date: Fri, 10 Jul 2009 17:36:30 +0100

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

2009/7/10 Jeffrey <>

> 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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Received on Fri Jul 10 2009 - 10:11:23 PDT
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