Re: Unable to calculate the entropy values in schlitter's of a protein system

[Nicholas M. Glykos]

You are trying to calculate the entropy of not just the solute (protein),
but of the whole system (with solvent and ions). You need to add a "-segid"
flag to define the protein component alone. Something like this should do
the trick :

./carma64 -v -w -fit -force -segid PROA -atmid ALLID newdcd-1.dcd newpsf.psf
./carma64 -v -cov -eigen -mass -force -temp 300 -atmid ALLID carma.fitted.dcd carma.selected_atoms.psf



On Tue, Oct 10, 2023 at 10:11:27AM +0530, Rabiul Gazi wrote:

> I have done MD simulation of a system that contains protein(2855 atom),
> alcohols, water and ions in NAMD.I want to calculate configurational
> entropy of the protein in Schlitter's method. I have used the following
> command.....
>
> 1===> ./carma64 -v -fit -force -atmid ALLID newdcd-1.dcd newpsf.psf > carma_entropy_after_newdcd-1.out
> 2===> ./carma64 -v -cov -eigen -mass -force -temp 300 -atmid ALLID carma.fitted.dcd newpsf.psf > carma_entropy_after_newdcd-2.out
>
> But I did not get any results. When I open the output file I got the following...
> ....
> Number of atoms in sets is 72526
>
> allocate failure 2 in matrix()
>
> Allocation errors mean that carma requested additional
> memory and the operating system refused to offer it.
> If your computing machine does have enough memory for
> the envisioned calculation, getting the 64bit GNU/Linux
> carma executable may be the solution to this problem.


--


Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, https://utopia.duth.gr/glykos/