Re: [AMBER] NPT at high pressure

From: Francesco Pietra <>
Date: Wed, 22 Aug 2012 16:36:37 +0200

Hi Jason:

It seems that some misplacing of your mail occurred. It can not be
related to my question about NPT at high pressure. In particular, in
my hands, NAMD-CUDA never crashed with parm7 on a multi GTX-680 cards.


On Wed, Aug 22, 2012 at 4:19 PM, Jason Swails <> wrote:
> On Wed, Aug 22, 2012 at 9:33 AM, Francesco Pietra <>wrote:
>> Hi;
>> I am using parm7 within NAMD. Is anything new with parm7 about
>> carrying out equilibration of a protein in a water box? I mean, water
>> model, flags? While range of temperatures have been explored, it seems
>> that ff have been devised for 1 bar. Nonetheless, these are
>> physiological conditions that would kill a deep water organism.
> I'm confused... Is NAMD not running (and complaining about a badly
> formatted topology file?). If it's 'running', then this is a question
> about parameters and force fields, not so much the topology file...
> If NAMD crashes, this is because NAMD does not adhere to the extensible
> Amber prmtop format specification. I haven't tested the latest version of
> NAMD, but NAMD 2.8 will not run with AmberTools12-generated topology file
> because a couple extra flags were added to the prmtop, but they can be
> deleted without much effort. The flags that are safe to delete (for use
> and IPOL.
> ParmEd can do this within its scripting environment, so a script that looks
> like this:
> !amber_prmtop.deleteFlag('ATOMIC_NUMBER')
> !amber_prmtop.deleteFlag('SCEE_SCALE_FACTOR')
> !amber_prmtop.deleteFlag('SCNB_SCALE_FACTOR')
> !amber_prmtop.deleteFlag('IPOL')
> outparm new_prmtop.parm7
> You will need to use the "-e" flag to allow python commands in ParmEd to
> use the above commands, though (note, ! is needed to activate the python
> interpreter for that command).
> HTH,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Aug 22 2012 - 08:00:02 PDT
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