AMBER Archive (2009)

Subject: Re: [AMBER] amber8 pmemd trajectory coordinates problem

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Oct 20 2009 - 20:03:37 CDT

I would have to look back at the code to remember exactly how it works, but
respa trajectories are indeed pulsed, I think in terms of the longrange
component. I don't think there is really that big a benefit associated with
using respa in reality (there are some issues involved in loadbalancing that
make it hard to fully benefit from only doing the longrange forces every
second or fourth step, given the way the code is currently written).
Regards - Bob Duke
----- Original Message -----
From: "Sergio Wong" <wong105_at_llnl.gov>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Tuesday, October 20, 2009 8:49 PM
Subject: Re: [AMBER] amber8 pmemd trajectory coordinates problem

> Hi;
>
> Thanks for the note. I think I should have said, every 4th SAVED
> trajectory step so that every 20,000, 1fs steps, is when the coordinates
> seem to move forward more than the previous 3.
>
> Thanks.
> -Sergio
> At 05:39 PM 10/20/2009, you wrote:
>
>> > I ran an explicit water simulation (TIP3P, PBC, counter ions,
>> > pme, etc) using PMEMD version 8. The problem is that when I visualize
>> > the trajectory it seems to advance very little except every 4th
>> > trajectory step. The system is of medium size ( 48732 Atoms) and my
>> > input file is below:
>>...
>>
>> > nrespa=4,
>>
>>If this problem is every 4th step, likely the NRESPA is the culprit.
>>
>>
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