Re: [gmx-users] Re: reasons for slow computation?

2011-10-11 Thread Mark Abraham
On 12/10/2011 3:48 AM, Yun Shi wrote: Hi Mark, I am not quite sure. While the "details" are different, I guess it is still valid to compare some statistical properties, right? For example, I should still be able to compare the average COM distance of these two ligands over long trajectories,

[gmx-users] Re: reasons for slow computation?

2011-10-11 Thread Yun Shi
Hi Mark, I am not quite sure. While the "details" are different, I guess it is still valid to compare some statistical properties, right? For example, I should still be able to compare the average COM distance of these two ligands over long trajectories, and make the conclusion that one is better

Re: [gmx-users] Re: reasons for slow computation?

2011-10-10 Thread Tsjerk Wassenaar
Hi Yun, For comparison, the conditions have to be equal. That does not include possible hardware issues. So you should be fine. Cheers, Tsjerk On Oct 11, 2011 4:41 AM, "Yun Shi" wrote: Hi Justin, I guess you are right, that some processors on that cluster appear to be much slower than others

Re: [gmx-users] Re: reasons for slow computation?

2011-10-10 Thread Mark Abraham
On 11/10/2011 1:40 PM, Yun Shi wrote: Hi Justin, I guess you are right, that some processors on that cluster appear to be much slower than others. More likely is that the mapping of processes to processors is faulty, as Justin said. But I am still wondering that, would the difference in

Re: [gmx-users] Re: reasons for slow computation?

2011-10-10 Thread Yun Shi
Hi Justin, I guess you are right, that some processors on that cluster appear to be much slower than others. But I am still wondering that, would the difference in initial maximum inter charge-group distances (0.451 nm vs 0.450 nm) and minimum initial size of DD gird (0.620nm vs 0.618nm) make the

Re: [gmx-users] Re: reasons for slow computation?

2011-10-10 Thread Justin A. Lemkul
Yun Shi wrote: And another difference I noticed from .log files are: .. Initial maximum inter charge-group distances: two-body bonded interactions: 0.451 nm, LJ-14, atoms 3586 4808 multi-body bonded interactions: 0.451 nm, Proper Dih., atoms 3586 4808 Minimum cell size due to

[gmx-users] Re: reasons for slow computation?

2011-10-10 Thread Yun Shi
And another difference I noticed from .log files are: .. Initial maximum inter charge-group distances: two-body bonded interactions: 0.451 nm, LJ-14, atoms 3586 4808 multi-body bonded interactions: 0.451 nm, Proper Dih., atoms 3586 4808 Minimum cell size due to bonded interactions