Re: [AMBER] problem in rmsd

From: Parimal Kar <>
Date: Mon, 9 Mar 2009 23:36:13 -0400

Hi Thomas,
    I output PDB files for each frame. interesting thing is when I
choose the option "new cartoon" in vmd, then the figure disappears.
But when i created the pdb file from the last rst file, it looks
reasonable while I visualize in VMD. What puzzles me, why these 3rd &
4th frame only give absurd rmsd irrespective of ntwx=1 or ntwx=50.
On Mar 9, 2009, at 11:25 PM, Thomas Cheatham wrote:

>> I am facing a weird problem while calculating the rmsd using
>> ptraj. I am doing the canonical simulation of TrpCage miniprotein at
>> 325k. I followed the steps available online (provided by ross
>> Walker ). After heating the system to the desired temperature, I
>> created a pdb file and it looks reasonable. Then I performed 100ps
>> short canonical MD at this temperature and stored the configuration
>> in every 50 steps (ntwx=50). While I calculated the rmsd of the
>> trajectory from the experimental nmr structure, I found that 3rd &
>> 4th snapshots give absurd rmsd (300+ AA). If I make ntwx=1, still I
>> found that 3rd & 4th snapshots gives absurd rmsd.
> 300+ Angstrom is indeed absurb. What I would do is output PDB
> files for
> each frame and look at them. Make sure there is not a mismatch in the
> prmtop/mdcrd; look at the energies over the simulation... --tec3
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Received on Wed Mar 11 2009 - 01:18:42 PDT
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