Dear yip,
The mdcrd files do not contain velocity information unless you set ntwv < 0 and you are using NetCDF.
>From Amber12 mannual page 20
Ntwv:
Every ntwv steps, the velocities will be written to the mdvel file. If ntwv = 0, no velocity trajectory file will be written. If ntwv = -1, velocities will be written to mdcrd, which then becomes a combined coordinate/velocity trajectory file, at the interval defined by ntwx. This option is available only for binary NetCDF output (ioutfm = 1). Most users will have no need for a velocity trajectory file and so can safely leave ntwv at the default. Default = 0.
Best,
Nitin
-----Original Message-----
From: Yip Yew Mun [mailto:yipy0005.gmail.com]
Sent: Wednesday, February 05, 2014 1:13 PM
To: AMBER Mailing List
Subject: [AMBER] Generating RST file using Cpptraj
Importance: High
Hi, I was generating a RST file using Cpptraj with the following input file:
trajin equ11.mdcrd 5000 5000
trajout equ11.rst restart
I was planning to use this RST file to continue my simulation. However, the velocities info was not written to it. Is there a way to resolve this problem? Thanks.
Regards
Yip Yew Mun
Graduate, PhD
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences Nanyang Technological University
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Received on Tue Feb 04 2014 - 23:30:03 PST
