Re: [gmx-users] Speeding up simulation

Large cut-offs can bring artificial artifacts. e.g. *Chemical Physics Letters* Volume 406, Issues 1-3

Re: [gmx-users] Speeding up simulation

That might actually be the best approach speed wise. But it depends on what level of accuracy you wish for your calculations. What is your system like? May be you can have a large cut off but you will have to see what the trade off between speed and accuracy is. On Wed, Aug 18, 2010 at 10:26 AM, m

Re: [gmx-users] Speeding up simulation

On 17/08/10 22:36, Justin A. Lemkul wrote: There is no way to limit PME to certain ranges. It is a method for solving infinite sums. Usually PME is a poor choice for in vacuo simulations and the like, since there's nothing to be done for most of the simulation box. This interests me -I've used

Re: [gmx-users] Speeding up simulation

Sapna, Is there a particular reason you're using a box so much larger than the droplet diameter? If your only concern is that periodic images should not see each-other maybe you can use a box length=droplet diameter+2*largest cut-off in the system. Also using a more spherical box shape such as r

Re: [gmx-users] Speeding up simulation

Hi Justin Thanks for your input. I guess I will do some more literature search and try to optimize the simulations as much as I can. Thanks, Sapna On Tue, Aug 17, 2010 at 5:36 PM, Justin A. Lemkul wrote: > > > sapna sarupria wrote: > >> Hi Justin >> Thanks for your response. I suspect that it

Re: [gmx-users] Speeding up simulation

sapna sarupria wrote: Hi Justin Thanks for your response. I suspect that it is the same thing. Is there a way to make gromacs use PME only within a certain region of the simulation box? Also, how does one know how to fix the load imbalances (in this context)? There is no way to limit PME t

Re: [gmx-users] Speeding up simulation

Hi Justin Thanks for your response. I suspect that it is the same thing. Is there a way to make gromacs use PME only within a certain region of the simulation box? Also, how does one know how to fix the load imbalances (in this context)? Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 P

Re: [gmx-users] Speeding up simulation

sapna sarupria wrote: Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much fast