Re: AMBER: non-isotropic pressure scaling

From: Lubos Vrbka <>
Date: Wed, 31 Mar 2004 21:44:19 +0200


> It would also be possible to patch pmemd 3.01 or better, 3.1 (which has
> better performance and scaling, and is available on the amber web site) to
> support this; you would need to look at the code in mdin_ctrl_dat.f90 and
> runmd_*.f90, and compare to equivalent code in sander 7 (and do comparison
> test runs to be sure you got it right).
i had a look into the source and compared sander7 to pmemd 3.1. i got
the impression that the only thing needed to get it running is to remove
the initial test (if ntp=2 print that it is not supported) in
mdin_ctrl_dat.f90, since ALL code that it is sander7 source (runmd.f,
step 7, ~line 1365) is present in pmemd 3.1 (runmd.f90, step 7, ~line
713). there are all the tests whether ntp .eq. 1 or ntp .gt. 1...

> The non-isotropic scaling
> capability is not in pmemd 3.01 - 3.1 because these programs were intended
> to be mostly sander 6 compatible, and it did not support non-isotropic
> scaling.
so could it be, that the feature was just disabled in pmemd for
compatibility reasons, but in fact is in the source "waiting to be

i'm not fortran programmer, so i may be wrong, but all the code
indicates to me that i might be right :)

thanks for your help. regards,

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Received on Wed Mar 31 2004 - 20:53:00 PST
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