Dataset Open Access

POPC_Ulmschneider_OPLS_Verlet_Group

Girych Mykhailo; Ollila O. H. Samuli

MD simulation trajectory and related files for fully hydrated POPC bilayer run with Verlet and Group schemes. The Ulmschneider force field for POPC was used with Gromacs 5.0.3 [1,2]. Conditions: T=298.15, 128 POPC molecules, 5120 tip3p waters. 200ns trajectory (preceded by 5ns NPT equillibration). Starting structure was obtained from CHARMM-GUI [3].

This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi

[1] J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813

[2] http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html

[3] http://www.charmm-gui.org/

Files (3.4 GB)
Name Size
confout_group.gro md5:c37af9b1545eda03e47c91a8d12984e1 1.5 MB Download
confout_verlet.gro md5:122d856b5d51b36740bb4202133a072a 1.5 MB Download
ener_group.edr md5:e0a1f8b8c27d0be0c45f8b00275806b8 63.6 MB Download
ener_verlet.edr md5:cad99b87a7b0b19defb7f3af673c8536 63.6 MB Download
mdout_group.mdp md5:9c917734c40e0408a4af2195ae2de92f 11.6 kB Download
mdout_verlet.mdp md5:f7db3313e4a3f10f99e2956bf5c3e584 11.6 kB Download
popc_opls.itp md5:fd3fbda2953e00e4a3f9e274502c236e 26.9 kB Download
popc_ulm_200ns_group.xtc md5:a1a985754f9d6759c586182849b9249c 1.6 GB Download
popc_ulm_200ns_verlet.xtc md5:fcbb0d11bce74598c1923ff528e4745d 1.6 GB Download
run_200ns_group.tpr md5:539205bb77fbd1336ed591da92d5331c 734.7 kB Download
run_200ns_verlet.tpr md5:44fcb319d98522568e238c5f2ec39d23 734.8 kB Download
run_POPC_group.mdp md5:89ce2f72c0f9fbc581f27ef01d14801b 1.2 kB Download
run_POPC_verlet.mdp md5:6ac650a88004f965bcc6501270a33941 1.2 kB Download
topol.top md5:1cf0552dc582d5da3976d8c6618e22eb 265 Bytes Download

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