From: Villalain Boullon, Jose (
Date: Wed Jun 05 2013 - 03:25:01 CDT

Dear All,


As a beginner to NAMD, I followed the membrane tutorial without any problem. I repeated it again but using a peptide, both inserted in the membrane and out of it. The configuration files are (nearly) identical, except for the system sizes, which are slightly different.


For the peptide out of the membrane it seems that there is no problem, the lipids and the peptide minimize and equilibrate as supposedly they would.


However, for the system with the peptide inserted in the membrane, the water layers change upon time from a rectangular box to a circle box, but the lipid membrane do not .


I have done it three times with the same result. I have checked the configuration files and do not see anything which might be wrong. Any hint to what might be incorrect?.


Thank you very much.



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