[gmx-users] why it is so slow

[Justin Lemkul]

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 
cutoffs.

> 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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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