Hi Sofia,
> 1. Any roughly approximation of the walltime for a membrane bound protein
> MD simulation? I could hardly find any publications describing the method
> using Lipid14 of Amber14.
>
The performance will be the same as a regular protein simulation - so count up the number of atoms you have and take a look at the benchmarks on the website - GPU benchmarks are here: http://ambermd.org/gpus/benchmarks.htm#Benchmarks - So if you had a 100K atom system and a Titan-X you could expect something in the region of 45 ns/day. Double that if you use a 4fs time step and hydrogen mass repartitioning.
> 2. During QM when you call gamess (&gms) in the input file, do you have to
> export the path to gamess first? Any relevant publications performing QM
> with AMBER14 and gamess DFT?
>
If you plan to do QM/MM using the external interface then the execution time will be dominated by the time to the QM calculation - you are then talking picoseconds a day at most - more likely a femtoseconds a day so be aware of this.
The external interface needs to know the path to Gamess - take a look at the external interface section of the manual: "http://ambermd.org/doc12/Amber15.pdf" (section 10). $GMS_PATH needs to be set to your Gamess installation location.
Here is the manuscript describing the external interface implementation: http://dx.doi.org/10.1002/jcc.23444
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Mon Sep 21 2015 - 00:30:03 PDT
