[gmx-users] output in gromos format

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 12 17:04:02 CEST 2010

grivet wrote:
> Hi everybody,
> In order to use an old set of analysis programs, I would like mdrun to
> ouput my trajectory in gromos-96 format. Is this possible ?

No, not directly.

> I understand that I could convert the .xtc file with trjconv. I need
> rather high precision, but I am uncertain about the meaning of the
> parameter xtc_precision; what does it mean?

The xtc_precision sets how many decimal places are written.  If you want really 
high precision, just convert the .trr file (provided you have enough disk space 
for all of its frames to start with).

> Another quite unrelated question; most examples I have looked at use
> rvdw = 1.0, regardless of the force field; however, the manual states
> that, with GROMOS force fields, one should use rvdw >= 1.4; which is
> correct ?

Per the parameterization of the force field (hint: read the primary literature), 
rvdw should be set to 1.4 nm.


> Thank you in advance for your help
> JP Grivet


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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