[gmx-users] Polymer melt clumping

Pallavi Banerjee pallavisept at students.iiserpune.ac.in
Sun Jul 12 12:38:58 CEST 2015

Hello users,
I am carrying out an NPT equilibration of a polymer melt system of 67
chains of Polyacrylamide of degree of polymerization 20. The polymer melt
system appears clumped. The system does not disperse throughout the box. To
tackle this, I adopted a method of scaling down the box vector by 0.95,
followed by an NPT run for 500 ps with a tau-p of 20. This I did for 6
number of times, and followed it up with a long NPT run of 10 ns with a
tau-p of 1.5. The system hasn't dispersed yet, and thus I do not get the
right density. How do you fix aggregation issues as this?

Thanks in advance,

Pallavi Banerjee.

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