[gmx-users] problem with equilibration of DLiPC membrane

Shiva Emami shemami at ucdavis.edu
Thu Nov 12 00:12:16 CET 2015


Dear all,

I'm a new Gromacs user and I'm trying to build a lipid membrane with 450 DLiPC (18:2) by using 43A1-S3 forcefield.

For membrane building, first I put  a single DLiPC molecule in small box, then replicated it in x-y by genconf -nbox to get 450 lipid molecules, then got another leaflet by editconf -rotate, followed by catting and combining two leaflets, EM, changing Z-dimension of the box,  solvation and EM.

When I equilibrate the membrane at lower temperature like 217 K it goes well. But trying equilibration at increased temperatures like 300 K, the membrane shrinks too much at NPT equilibration and area per lipid decreases to very low values.

Can anybody help me in this case?

Many thanks


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