[gmx-users] gmx mindist issue

[Carlos Navarro Retamal]

Nobody know what may be happening?
Thanks in advance,
Carlos

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Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl



On March 23, 2015 at 1:33:03 PM, Carlos Navarro Retamal (cnavarro at utalca.cl<mailto:cnavarro at utalca.cl>) wrote:

Dear gromacs users,
I’m performing CG simulations in order to analyse the interactions between two proteins (proteins A and B ) and an specific membrane. To measure this interactions i’m using two different approach.
1.- i’m measuring the RDF (using VMD) between the proteins and an specific atom of the membrane (C1 atom in a MGDG membrane)
2.- Using gmx mindist i want to measure the contacts between; again, the proteins and the respective atom of the membrane (again C1 atom in MGDG).
During the simulation i notice how the protein A possess a higher affinity with respect to the membrane, and by using the first approach, i got a nice correlation, having a bigger pick for the protein A at a distance of 0.5 nm.
My problem arise using gmx mindist as following:
gmx mindist -f dynamicCG_500ns_all.xtc -s dynamicCG_500ns.tpr -n index.ndx  -o test.xvg

Using the above command line, i got a bigger amount of contacts between the protein B and the membrane (~4000) rather the protein A and the membrane (~2000), which doesn’t make any sense, since that i saw how A is able to interact in a better and longer way than B.

How should i properly use gmx mindist?

Best regards,

Carlos

--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl