AMBER Archive (2006)

Subject: Re: AMBER: Is GB/SANDER slower than TIP3P/PMEMD

From: Robert Duke (
Date: Wed Oct 04 2006 - 12:45:06 CDT

Yuming -
PMEMD supports both frozen (ibelly-based) and restrained (ntr-based)
simulations. What it does not support is the new way of specifying the
belly or restrained atoms - the restraint_wt, restraintmask, and bellymask
keywords to the &cntrl namelist section. Instead, you must use an older
amber-style GROUP specification; how to do this is specified in Appendix B
of the amber 6, 7, or 8 manuals; it unfortunately was dropped from the amber
9 manual (trying to cut the size down, I think). As far as pmemd being
faster running pme than sander running gb, I would guess it depends on
various performance-related options one might choose (like gb cutoffs,
nrespa); pmemd also does generalized Born as of amber 9, and is generally
also a bit faster than sander for gb, depending on machine, math libraries,
etc. etc. For small systems, I think there are not a lot of impediments to
using pme these days in terms of performance. However, gb can be used for
gbsa and mmtsb under sander but not under pmemd.
Regards - Bob Duke

----- Original Message -----
From: <>
To: <>
Sent: Wednesday, October 04, 2006 1:21 PM
Subject: AMBER: Is GB/SANDER slower than TIP3P/PMEMD

>I have some questions about SANDER and PMEMD. I tried to run GB simulation
> SANDER and also tried the TIP3P water simulation by PMEMD. The system is
> a 100 residues protein(charge +9) and the water number is ~8000. The
> much slower than the TIP3P/PMEMD. It surprised me because I always think
> that
> implicit solvent is much faster than explicit one. Is it due to the
> different
> between PMEMD and SANDER? If it is, is there any way to run the GB
> simulation
> with higher speed?
> The other thing is that PMEMD seems not support the ibelly simulation,
> which can fix specific part of protein. Is there any way to do it? Thank
> you.
> Yuming Morris Chen
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