[gmx-users] REMD speed calculation compared to classical MD
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 13 20:27:04 CEST 2010
On 10/13/10 7:42 PM, XAvier Periole wrote:
> Well the exchanges do not cost time ... so basically each replica runs
> at the speed it would run it was a regular simulation on the number of
> cpu you give each replica.
> I do not think there any significant difference in NPT/NVT simulations.
> Note NVT is often used for REMD
It us, but that gives high pressure at high T, which is typically not
what you want.
If you use NPT REMD than the run time between exchanges is in general
equal to that of the coldest replica, since that will be at the highest
density (unless you go below the density maximum of water :)).
> On Oct 13, 2010, at 11:36 AM, ABEL Stephane 175950 wrote:
>> Dear All,
>> For a futur project, I would like to perform the REMD calculations
>> with GROMACS4.5.X. To have an estimation of CPU time required, I have
>> a naive question: What is the speed of REMD compared to a classic NPT
>> MD ? I am aware that the response depends a lot of factor (number of
>> replica, etc.), but since i have no idea and experience with this type
>> of MD, I ask the question ;).
>> The system will have approximatively 25000 atoms. Previously for this
>> system, I got 11 ns/day on 32 CPU for a NPT MD with GROMOS53A6 and
>> Thanks you in advance for your response.
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David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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