Re: [AMBER] Generating RST file using Cpptraj

From: Nitin Sharma <sharmanitin.nus.edu.sg>
Date: Wed, 5 Feb 2014 15:24:51 +0800

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
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