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 replicating it in x-y by genconf -nbox, getting another leaflet by editconf -rotate, changing Z-dimension of the box, EM, 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
How much is too much? Shrinking is bound to happen since creation of membranes usually leaves vacuum between sections. I believe at this oddly chosen temperature of 217K, your system still doesn't have enough energy to show the reduction in the area which becomes significantly pronounced at 300K.
Do you heat your system?
Why did you use 217K why not 220K?
One can assume that when the area per lipid converges you have a equilibrated membrane. Do you have an idea what this should be? Or do you just guess that the area per lipid is decreasing too much?
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