Re: AMBER NetCDF file for Simulation

From: Brian Radak (
Date: Thu Jun 07 2018 - 09:18:39 CDT

Hmm. I do not see how this would be attributed to either the file format or
minimization instability. Am I missing some piece of information from the
ENERGY output?

Are you using periodic boundary conditions? The second image looks cubic,
but I cannot tell in the first. Extensive minimization will generally have
issues with wrapping when using PBCs. There may also be some issue with the
way the cellBasisVectors and origin are being specified. If I recall
correctly, the AMBER conventions are a bit different from those NAMD
inherited from XPLOR.

Can you list the relevant settings from your input file?

On Thu, Jun 7, 2018 at 8:50 AM, Aashish Bhatt <>

> Dear Sir
> I have attached two image
> one image is
> >>D*id you load the prmtop and restart files and then save as a pdb?* >>
> I have load prmtop and restart file and then save PDB for coordinate(
> *file.pdb).*
> *initial structure*
> *and second image is minimization image.*
> *Regards*
> *Aashish Bhatt*
> On Thu, Jun 7, 2018 at 6:08 PM, Brian Radak <> wrote:
>> Is the problem with how VMD and/or NAMD handle your NetCDF formatted file
>> or is the problem that the minimization is unstable?
>> If the problem is the second of these, can you be more specific about
>> what you mean by unstable? Is there an error message or does something just
>> not look as expected?
>> ‚Äč

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