[gmx-users] why it is so slow

Justin Lemkul jalemkul at vt.edu
Fri Nov 2 16:12:17 CET 2012

On 11/2/12 11:08 AM, Albert wrote:
> On 11/02/2012 04:02 PM, Justin Lemkul wrote:
>> I wasn't suggesting that you use NPT, I was merely pointing out that you made
>> an statement that wasn't true and thought I would mention it.
>> It looks like you have other issues to deal with.
>> -Justin
> Hello Justin:
>   thanks a lot for such kind reply.
>   What's the left problems are there? I just remember that in an old gromacs

The problem I was referring to was the fatal error in your last mail.

> mailist thread some one mentioned that NPT would be better for REMD. However, I

Quite the opposite.  You can get very different densities, depending on the 
range of temperatures, that can cause various algorithms to fail.

> am using GBSA solvent model, do you think NPT is also better than NVT?

No.  In fact, using GBSA, you should be using a non-periodic cell with infinite 

> I never done REMD before.

It would be wise, then, to spend a significant amount of time reading before 
attempting anything.  A few hours spent in the literature will potentially save 
you weeks of wasted CPU time if you realize you're not doing something right.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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