VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Aug 30 2014 - 11:22:28 CDT

this is a question about a gromacs tool and has no connection to VMD.
please ask on the gromacs users mailing list, which is the right place
to ask.

On Sat, Aug 30, 2014 at 5:19 PM, sunyeping <sunyeping_at_aliyun.com> wrote:
> Dear all,
>
> I am using g_anaeig to calculate entropy from the MD trajectory. Firstly I
> got eigenvec.trr by g_covar command, and then used the following command:
>
> g_anaeig -s md_0_1.tpr -v eigenvec.trr -b 0 -e 225 -n index.ind -entropy
>
> However, I didn't got the entropy values. The output was:
>
> .......... ............
> eigval[1090] = -1.44331
> eigval[1093] = -1.35067
> eigval[1096] = -1.02231
> eigval[1099] = -0.962267
> eigval[1102] = -1.02198
> eigval[1105] = -0.775765
> eigval[1108] = -0.51662
> eigval[1111] = -0.542334
> eigval[1114] = -0.431655
> eigval[1117] = -0.163827
> eigval[1120] = -0.00552675
> The Entropy due to the Quasi Harmonic approximation is inf J/mol K
> The Entropy due to the Schlitter formula is nan J/mol K
> Reading file md_0_1.tpr, VERSION 5.0-dev (single precision)
> Reading file md_0_1.tpr, VERSION 5.0-dev (single precision)
> 1 eigenvectors selected for output: 1
>
>
> Could you tell why why the entropy cannot be calculate properly?
>
> Best regards.
> .
>
> Yeping 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.