Thanks very much for the information.
I initially used the Langevin thermostat as per the AMBER tutorial, but it took ages to get 100 steps on the GPU. Switched to Berendsen and the GPU simulation ran noticeably faster. I have not got the timings to hand, but I'm guessing a x2 speed increase at least. However, as mentioned I don't think I can use this thermostat with implicit solvent. As the structure has 47,000 atoms, do you think the difference between Anderson and Langevin will be more pronounced due to the system size? I'm hoping so, as the simulation will be painfully slow otherwise. Also do you know what is a good setting for vrand?
I'm not familiar with using nmropt to guide the equilibration temp. Hope you don't mind me being cheeky, but could you possibly cut and paste a sample of your input file to provide some guidance? Don't worry about it if it is inconvenient though.
The RMSD idea sounds good. I'll try it out.
Thanks again!
On 26 Mar 2015, at 05:56, Hai Nguyen <nhai.qn.gmail.com<mailto:nhai.qn.gmail.com>> wrote:
Hi,
Like Jason's case, I have been using Langevin (ntt=3) for implicit solvent
(GB) and have no problem with its speed.
You can see our benchmark (up to 100 residues), equil protocol, speend
(ns/day) ... in the supp of our paper:
Folding Simulations for Proteins with Diverse Topologies Are Accessible in
Days with a Physics-Based Force Field and Implicit Solvent
<
http://pubs.acs.org/doi/abs/10.1021/ja5032776>
you can vary the gamma_ln value to reduce/increase the 'viscosity' in your
simulation. Smaller number will significantly increase your sampling speed
while keeping the same thermodynamic property.
On Wed, Mar 25, 2015 at 7:41 PM, Glenn Carrington [bs10g3c] <
bs10g3c.leeds.ac.uk<mailto:bs10g3c.leeds.ac.uk>> wrote:
Dear Amber users,
I'm planning to run a large implicit solvent simulation of myosin using
AMBER 12. I had a few questions that I was hoping someone could help me
with.
1 - The molecule is quite big and I plan to use GPU's. The tutorials i
looked at use a Langevin thermostat, but the GPU page states that this is
very inefficient and I should use the Berendsen or Anderson thermostats. As
the AMBER manual rules out the Berendsen due to issues with implicit
solvent model, I guess I'm stuck with the Anderson (ntt=2). Could anyone
with experience let me know the best setting for vrand (other than the
default of 1000?) From what I've read this is the only variable associated
with the Anderson thermostat?
(check my reply above)
btw, don't expect to see dramatically speedup in the speed for implicit
solvent MD with large system (in term of ns/day you get) vs explicit water
MD. The benefit of speeding up is in sampling efficiency (check posted
paper).
2 - What settings do people use to equilibrate an implicit solvent
simulation? Is the only consideration increasing the temperature from 0K to
the target temp?
We posted our equil protocol in the paper above. Generally, the equil
protocol depends on your system. For example if you need to use another
program (like tleap) to build extra sidechain, residue, you might want to
restraint other part of you system and relax the built part first in your
equil.
In our experience, increasing T from 100K to targeted T is better choice
than 0K.
3 - Parts of the structure I'm using has been homology modelled. Are there
any established protocols that anyone is aware of that I could use to test
the stability of my structure?
(no comment)
Hai
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Received on Thu Mar 26 2015 - 05:30:02 PDT
