Re: [AMBER] writing trr trajectory

From: Daniel Roe <>
Date: Wed, 1 Oct 2014 08:11:50 -0600


Unfortunately I'm not sure what is going on since I'm not very
familiar with gromacs. My test that I was writing gromacs trajectories
correctly was to read them in VMD as well - clearly I need to do some
more testing.

However, if I understand you correctly it is possible to generate
pseudo-trajectories along different eigenvectors with cpptraj. For
example, if you have the output from a previous 'diagmatrix' command
named 'evecs.dat' and you originally generated the covariance matrix
with the mask ':1-20&!.H=' and the topology 'myparm.parm7' you can
generate a pseudo trajectory along the first eigenvector like so:

parm myparm.parm7
readdata evecs.dat name myevecs
runanalysis modes trajout name myevecs trajout trajoutfmt netcdf
trajoutmask :1-20&!.H= pcmin -20 pcmax 20 trajmode 1

You can adjust pcmin and pcmax to appropriate values by looking at the
min/max projection values you get from the 'projection' action.

Hope this helps,


On Tue, Sep 30, 2014 at 5:16 PM, newamber list <> wrote:
> Hi,
> Just to add in specific I need to do some functionality available in
> gromacs (g_anaeig) to "calculate the two extreme projections along a
> trajectory on the average structure " which provides two extremes as pdb.
> If it is possible with cpptraj then I dont need to convert in trr (but will
> be worth knowing whats the issue)
> Thanks
> On Tue, Sep 30, 2014 at 11:50 PM, newamber list <>
> wrote:
>> Dear All
>> I am converting my amber traj netcdf to gromacs trr file with cpptraj.
>> When I use trr for some analysis in gromacs I get error (in gromacs) that
>> atoms does not match which I have checked is not an issue.
>> I suspect this might be due to absence of velocity info in my amber traj
>> netcdf and trr should have velocity and force information. How cpptraj
>> considers this while writing trr? I mean does it keep the original format
>> of trr even if velocity info is missing in netcdf file. May be this is
>> reason why gromacs can not find enough points in trr file. But again the
>> trr file written by amber is read fine with vmd.
>> thanks
>> Jio
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Wed Oct 01 2014 - 07:30:02 PDT
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