Re: NAMD is too slow?!

From: DimitryASuplatov (genesup_at_gmail.com)
Date: Sun Mar 29 2009 - 12:23:05 CDT

Thanks for your replies.

> it would be helpful to know the dimensions of your system and the total
> number of atoms. Are you using timestepa nd multiple timestepping
> parameters equivalent to those in the simulations in gromacs that you're
> comparing to?

Dimensions:
min {9.51000022888 -37.9959983826 -20.3080005646}
max {118.291000366 64.4000015259 84.8870010376}
center 63.87940979 13.3578186035 32.2524185181
timestep 2fs

>
> Also, you're using the wrong compilation target -- you've compiled for
> itanium, and thus have probably missed out on some compilation flags
> that would significantly improve your performance. You want to be using
> Linux-x86_64 as a base architecture. You can probably use more
> aggressive compilation options since you're running on xeons -- adding
> -xT -DNAMD_SSE
> to the FLOATOPTS in your .arch file should help. Are you using namd 2.7b1?
>

Thanks. I`l try using those

> Also... why are you running without PME? Aside from the fact that long
> range electrostatics are generally important in proteins, in my
> experience MD water models don't do well with shifted electrostatics...
>

To my understanding using PME is sufficient with periodic systems -
like lipid membranes - and could overstabilize free energy when used
with proteins.

SDA

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