Protein moving out of water-box after 10 ns simulation

From: Jie-rong Huang (
Date: Wed Feb 27 2008 - 08:13:24 CST

Dear NAMD users,

I run a script (as used in tutorial) with 10 ps minimization and then run
for 10 ns for ubiquitin with 15 Na and 15 Cl randomly added by "Add Ions"
plug-in. However, in the end of 10 ns, part of the protein came out of the
water-bax (I used "solvate" with layer 8A). How I can keep the protein in
the middle of water box during the long trajectory simulation? Only way I
can think about is put

fixedAtoms on
fixedAtomsForces on
fixedAtomsFile ubiquitin.pdb #column B of a few residue (maybe 1 or 2) are
fixedAtomsCol B

However, this "going-out" problem might only be caused by some parameter
Can anyone give me some suggestions?


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