Re: [AMBER] GaMD patches to Amber 14 and PME's gridhi parameter

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Wed, 16 Nov 2016 15:36:06 +0000

Dr. Case,

Thank you very much! Will go ahead with rebuilding. Amber 16 in on order.

Best regards, Voytek Kasprzak

Wojciech (Voytek) Kasprzak (Contractor)
Analyst Programmer,
Basic Science Program,
Leidos Biomedical Research, Inc.
Frederick National Laboratory for Cancer Research (FNLCR)
Frederick, MD 21702
(301) 846 5537

From: David A Case []
Sent: Wednesday, November 16, 2016 9:56 AM
To: AMBER Mailing List
Subject: Re: [AMBER] GaMD patches to Amber 14 and PME's gridhi parameter

On Wed, Nov 16, 2016, Kasprzak, Wojciech (NIH/NCI) [C] wrote:
> Earlier this year we modified the gridhi parameter in Amber 14
> mdin_ctrl_dat.F90 source file to 1024 in order to deal with very large
> solvent boxes (PME calculations). Recently our applications manager
> patched Amber 14 with the GaMD sources and noticed that gridhi is no
> longer defined in the mdin_ctrl_dat.F90 source file. It is now defined
> in mdin_ewald_dat.F90 and set to the default value of 512.
> Can we change this parameter to 1024 without interfering with the
> Gaussian accelerated MD patches?

This is confusing: the gridhi variable has never (as far as I know) been
in mdin_ctrl_dat.F90. Certainly in both amber14 and amber16 it is defined
in mdin_ewald_dat.F90.

Having said that, I would guess that modifying gridhi would not break
anything; of course, you should check.

Consider upgrading to amber16. Then you won't have to apply patches or worry
about code diversion: GaMD is now a standard part of pmemd.


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