I have a surfactant bilayer composed of two different types of surfactant molecules (total number of surfactant atoms= 3400). The bilayer is in ripple phase and I wanted to separate out the leaflets.
For this, I have used "fatslim membranes" command and provided a trajectory file, an index file of headgroups and a reference structure file. For output, I am using --output-index option. As a result, I get index files at each time frame where atoms contributing to leaflet 1 and 2 are written.
But at few time frames (for example at frame 1962), I get incorrect number of atoms as the sum of surfactant atoms is not equal to 3400. On visualising the structure obtained using the atom index at this frame, many molecules of the upper leaflet are missing.
Next, if I look at the successive time frame 1963, the structure looks fine. For this time frame, fatslim generates correct index and the total number of atoms are 3400.
I do not understand why fatslim does not generates correct index at certain frames as many of the molecules are missing.
Here I am attaching the snapshots of reference structure, the snaphot of bilayer at frame 1962 (where fatslim gives incorrect index) and snapshot of next time frame, 1963 (which looks fine). Kindly see the attachments and please help me to fix this problem.
Dear FATSLiM users,
I have a surfactant bilayer composed of two different types of surfactant molecules (total number of surfactant atoms= 3400). The bilayer is in ripple phase and I wanted to separate out the leaflets. For this, I have used "fatslim membranes" command and provided a trajectory file, an index file of headgroups and a reference structure file. For output, I am using --output-index option. As a result, I get index files at each time frame where atoms contributing to leaflet 1 and 2 are written.
But at few time frames (for example at frame 1962), I get incorrect number of atoms as the sum of surfactant atoms is not equal to 3400. On visualising the structure obtained using the atom index at this frame, many molecules of the upper leaflet are missing. Next, if I look at the successive time frame 1963, the structure looks fine. For this time frame, fatslim generates correct index and the total number of atoms are 3400. I do not understand why fatslim does not generates correct index at certain frames as many of the molecules are missing. Here I am attaching the snapshots of reference structure, the snaphot of bilayer at frame 1962 (where fatslim gives incorrect index) and snapshot of next time frame, 1963 (which looks fine). Kindly see the attachments and please help me to fix this problem.